BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0002.0552.p (765 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 1379 0.0 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 854 0.0 gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 95 2e-20 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 79 2e-15 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 1379 bits (3569), Expect = 0.0, Method: Compositional matrix adjust. Identities = 657/766 (85%), Positives = 713/766 (93%), Gaps = 2/766 (0%) Query: 1 VLLGGIGVLVALVLMAVLVLGFVVTLAYPKLPDLDTLTDYRPKIPLRVFSADGVLIGEFG 60 +LLG +G + L +M +L + F+V L YPKLPDLDTLTDYRPKIPLR+FSADGVLIGEFG Sbjct: 7 ILLGLVGTIFGLAVMVLLGVTFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGVLIGEFG 66 Query: 61 EERRNLVHIKDIPDIMKKAVLAIEDDRFYEHGGVDYQGIVRASVANLSGGGGGASTITQQ 120 EERRNLVH KDIP+IMKKAVLAIEDDRFYEHGGVDYQGI RA+ +NLSGGGGGASTITQQ Sbjct: 67 EERRNLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGGGGASTITQQ 126 Query: 121 VARNFFLTSNEPTFLQKASRKFLYEIPLAWKIERNLTKDQILEVYMNQIYLGQRAYGFSS 180 VARNFFLTSNEPTFLQKA+RKF YEIPLAWKIE NLTKDQILEVYMNQIYLGQRAYGF+S Sbjct: 127 VARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFAS 186 Query: 181 AAQIYFGKQLKELTIAESAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDA 240 AAQIYFGKQLK+LTIAE+AMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDA Sbjct: 187 AAQIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDA 246 Query: 241 QYTQAKDEELKVKTDSTAFGVHAEYVSEMARQLVYAQFKDDTYTRGLNVFTTITKADQDA 300 QY AKDEEL+VK DS+AFG+HAEYV+EMARQLVYAQ+KD+TYTRGLNVFTTITK DQDA Sbjct: 247 QYQAAKDEELRVKGDSSAFGMHAEYVAEMARQLVYAQYKDETYTRGLNVFTTITKTDQDA 306 Query: 301 AYLALRRGIIDYERRHGYRGPEGYMEIP-TASKEEADDAIESELADHPDSDDLIAAVVLE 359 AY+ALRRGIIDYERRHGYRGPEGYM++P A+K+ +DA+E ELADHPDSDD+++AVVLE Sbjct: 307 AYIALRRGIIDYERRHGYRGPEGYMDLPENATKDAVEDAVEVELADHPDSDDMVSAVVLE 366 Query: 360 ATTKEITAVLATGDEIKISGAGLGFAGNLLSEKAPPQKKIKRGAIIRVFQDGKNWIVTQM 419 A KEITA+L+TG+EI ISGAGLGF NLLS+KAPPQKKI+RGAIIRVFQDG NWI+TQM Sbjct: 367 AKPKEITAMLSTGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDGNNWIITQM 426 Query: 420 PEVESAFISLDPNDGSIRSLVGGFDFNRNKFNHVIQAWRQPGSSFKPFIYSSSLEKGLSP 479 PEVESAF+S++ DG+IRSLVGGFDFNRNKFNHV QAWRQPGSSFKPFIYSSSLEKGLSP Sbjct: 427 PEVESAFVSVNSQDGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSLEKGLSP 486 Query: 480 ATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQE 539 ATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQE Sbjct: 487 ATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQE 546 Query: 540 YITRFGFDADKNPPYLTLALGAGAVTPLQMVGAYSVFANGGYKINPYLISKITDNNGNTL 599 YITRFGFDADKNPPYLTLALGAG VTPLQMVGAYSVFANGGYKINPYLI+K+TD+NG L Sbjct: 547 YITRFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTDSNGEVL 606 Query: 600 SEAHPARSGDEANRVIDPRNAFVMDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDSMD 659 S+A PA + DE+NRVID RNAF+MDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDSMD Sbjct: 607 SQAKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDSMD 666 Query: 660 AWFAGYQPNLVGIAWMGYDQPKSLGDRETGGGLALPIWISYMQKALKDVPMVDRTVPGGL 719 AWFAGYQP L IAW+GYDQPKSLGDRETGGGLALP+WISYM KALKDVP VDR VP GL Sbjct: 667 AWFAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDRKVPDGL 726 Query: 720 IESGGEYYYSEYPPSASVRDLGLGEHGAAASPEEEKAKNQMKNELF 765 IESGGEYYY+E+PPSA VRDLG+G+ + +PEEEKAK QMKNELF Sbjct: 727 IESGGEYYYAEFPPSAMVRDLGMGDR-SGLTPEEEKAKTQMKNELF 771 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 854 bits (2206), Expect = 0.0, Method: Compositional matrix adjust. Identities = 439/737 (59%), Positives = 557/737 (75%), Gaps = 17/737 (2%) Query: 3 LGGIGVLVALVLMAVLVLGFVVTLAYPKLPDLDTLTDYRPKIPLRVFSADGVLIGEFGEE 62 L +G+ VA L+ V L F+ P+LP L+ +TDYRPK+PLR++S D VL+GEFGEE Sbjct: 31 LSILGLGVAGALLVVYALIFI----NPRLPSLELITDYRPKVPLRIWSEDKVLLGEFGEE 86 Query: 63 RRNLVHIKDIPDIMKKAVLAIEDDRFYEHGGVDYQGIVRASVANLSGGGG--GASTITQQ 120 +R+LV + DIP MK AVLAIED RFYEHGG+D+ GI RA V ++ G GASTIT Q Sbjct: 87 KRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTITMQ 146 Query: 121 VARNFFLTSNEPTFLQKASRKFLYEIPLAWKIERNLTKDQILEVYMNQIYLGQRAYGFSS 180 VARN FLT E TF SRK LYE+ LA KIE LTKDQILEVYMNQIYLGQRA+GF++ Sbjct: 147 VARNVFLTK-EKTF----SRK-LYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFAA 200 Query: 181 AAQIYFGKQLKELTIAESAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDA 240 AA+ YFGK LK++T+AE+AMLAGLPKAPSAYNP+VNPKRAH RQQYIL RM +G+IT A Sbjct: 201 AARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQRMLDVGFITKA 260 Query: 241 QYTQAKDEELKVKTDSTAFGVHAEYVSEMARQLVYAQFKDDTYTRGLNVFTTITKADQDA 300 QY +A EELKV+ + + +HAEYV+EM RQ+VYAQ+K+DTYT+G NV+TT+ ADQ A Sbjct: 261 QYEKAAKEELKVRAPGSQYNIHAEYVNEMVRQMVYAQYKEDTYTQGFNVYTTVNAADQQA 320 Query: 301 AYLALRRGIIDYERRHGYRGPEGYMEIPTASKEEADDAIESELADHPDSDDLIAAVVLEA 360 AYLA+R+G++DY+RRHGYRGPE +E+P A+ E+ AI+ + DHPD+DD++AAVV+ A Sbjct: 321 AYLAVRKGVMDYDRRHGYRGPEETIELP-ANAEDRAAAIDDVMDDHPDNDDILAAVVVAA 379 Query: 361 TTKEITAVLATGDEIKISGAGLGFAGNLLSEKAPPQKKIKRGAIIRVFQDGK-NWIVTQM 419 + K+I AVL +GD+I I G L F + LSEKA +I GA+IRV QD K NW V Q+ Sbjct: 380 SPKQIDAVLRSGDKISIKGEALRFVASALSEKAKKDIRIGPGALIRVMQDAKQNWQVAQL 439 Query: 420 PEVESAFISLDPNDGSIRSLVGGFDFNRNKFNHVIQAWRQPGSSFKPFIYSSSLEKGLSP 479 P+VE+A +S+ P DG+IR+LVGGFDF +N FNHV QAWRQPGS+FKPFIYS++LEKG +P Sbjct: 440 PQVEAALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQPGSTFKPFIYSAALEKGFAP 499 Query: 480 ATIINDAPLTFTQTGGQV-WQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQ 538 A+I+NDAP+++ GQ W+P++ GPI++R ALQKS+NLV+IR L+ +GV YA+ Sbjct: 500 ASIVNDAPVSYPAGPGQPNWEPRD-DETPAGPITVRTALQKSVNLVAIRTLDYIGVPYAK 558 Query: 539 EYIT-RFGFDADKNPPYLTLALGAGAVTPLQMVGAYSVFANGGYKINPYLISKITDNNGN 597 ++IT +GFDADK PPYL +ALGAG PLQ+ AYSVFANGGYK+ PYLIS+ITD G Sbjct: 559 DFITGTYGFDADKVPPYLPMALGAGQTNPLQLSAAYSVFANGGYKVQPYLISQITDARGQ 618 Query: 598 TLSEAHPARSGDEANRVIDPRNAFVMDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDS 657 LS+A P G+ A RV+ RN+++M SML+ V + GT ++ S+ R+DLAGKTGTTND+ Sbjct: 619 ALSKAEPLIVGNGAPRVVSERNSYMMTSMLKSVAQGGTGARSNSIGRSDLAGKTGTTNDA 678 Query: 658 MDAWFAGYQPNLVGIAWMGYDQPKSLGDRETGGGLALPIWISYMQKALKDVPMVDRTVPG 717 +D WFAGYQ L + WMGYDQPKSLG +E G LALPIW+ YM KALK VP D VP Sbjct: 679 VDGWFAGYQRTLATVVWMGYDQPKSLGSKEFGAQLALPIWVDYMAKALKGVPQFDLPVPE 738 Query: 718 GLIESGGEYYYSEYPPS 734 G+ GE YY + P+ Sbjct: 739 GIRFIDGEPYYDNFTPN 755 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 83/287 (28%), Positives = 138/287 (48%), Gaps = 23/287 (8%) Query: 423 ESAFISLDPNDGSIRSLVGGFDFNRNKFN-HVIQAWRQPGSSFKPFIYSSSLEKG-LSPA 480 + A I +D G + + VG N + A RQ GS+ KPF+Y ++EK L+ A Sbjct: 307 DGAIIVIDNATGDVLAWVGSSGPLSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAA 366 Query: 481 TIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQEY 540 ++++D+P+ + G ++ P+NY +++G +S+R +L S+N+ ++R L V + Sbjct: 367 SLLDDSPVNLATSAG-LYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPERFFRR 425 Query: 541 ITRFGFDADKNPPY--LTLALGAGAVTPLQMVGAYSVFANGGYKINPYLISKITDNNGNT 598 + GF+ ++ Y +LALG+ VT + AY V AN G + P L +++ + Sbjct: 426 LQALGFNLRESGDYYGYSLALGSADVTLANLANAYRVLANQG-RYTP-LRTRLDE----- 478 Query: 599 LSEAHPARSGDEANRVIDPRNAFVMDSMLRDVVRHGTAV---KALSLKRTDLAGKTGTTN 655 AR+ A +V+D A+++ +L D ALS R A KTGT+ Sbjct: 479 ------ARTPARATQVMDADAAYIVGDILSDRSARARTFGLENALS-TRIWTAVKTGTSK 531 Query: 656 DSMDAWFAGYQPNLVGIAWMGYDQPKSLGDRETGGGLALPIWISYMQ 702 D D W GY W+G + D +G A P+W MQ Sbjct: 532 DMRDNWCVGYSTRYTVGVWVGNASGAPMWD-VSGVTGAAPVWQEVMQ 577 Score = 85.1 bits (209), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 55/173 (31%), Positives = 88/173 (50%), Gaps = 15/173 (8%) Query: 61 EERRNLVHIKDIPDIMKKAVLAIEDDRFYEHGGVDYQGIVRASVANL-SGGGGGASTITQ 119 E + V ++D+ ++ A++A ED RFY+H G+D+ + ++ NL + GASTIT Sbjct: 61 ERKLAWVRLEDVSPALRHALIASEDRRFYQHSGIDWSAVAASAWGNLWNSKTRGASTITM 120 Query: 120 QVA----RNFFLTSNEPTFLQKASRKFLYEIPLAWKIERNLTKDQILEVYMNQIYLGQRA 175 Q+A + S + QK S+ ++ + +ERN KDQILE Y+N + Sbjct: 121 QLAGLIYDDLRRKSGARSLTQKVSQAWIAQ-----SLERNWRKDQILEAYLNLVAFRGEL 175 Query: 176 YGFSSAAQIYFGKQLKELTIAESAMLAGLPKAPSAYNPVVNPKRAHARQQYIL 228 G + ++I FGK L E+A+ L +AP+A P+R R IL Sbjct: 176 VGVHALSRIMFGKHPSGLDQGEAAIAVALIRAPNA-----TPRRVADRACAIL 223 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 78.6 bits (192), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 55/162 (33%), Positives = 83/162 (51%), Gaps = 8/162 (4%) Query: 72 IPDIMKKAVLAIEDDRFYEHGGVDYQGIVRASVANLSGGG--GGASTITQQVARNFFLTS 129 I + +K+A++A ED F H GVD++ + +A N G G STITQQ+A+N FL S Sbjct: 70 ISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQLAKNLFL-S 128 Query: 130 NEPTFLQKASRKFLYEIPLAWKIERNLTKDQILEVYMNQIYLGQRAYGFSSAAQIYFGKQ 189 E ++L+K E + + +E L K +I E+Y+N + G +G +AAQ Y+ Sbjct: 129 GERSYLRKGQ-----EFIITYMLEFLLDKQRIFEIYLNVVEWGNGVFGAEAAAQHYYRIP 183 Query: 190 LKELTIAESAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRM 231 L ++A LA + P Y+ AR IL RM Sbjct: 184 AASLGAEQAARLAVMLPRPRYYDRNRGSGYLAARTSLILRRM 225 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.317 0.136 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 2,382,440 Number of extensions: 104462 Number of successful extensions: 304 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 292 Number of HSP's successfully gapped: 6 Length of query: 765 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 672 Effective length of database: 1,179,515 Effective search space: 792634080 Effective search space used: 792634080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 134 (56.2 bits)