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= 0005.0276.p (261 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313642|ref|YP_003777734.1| arogenate dehydratase [Herbaspi... 387 e-109 gi|300313886|ref|YP_003777978.1| amino acid ABC transporter peri... 74 1e-14 gi|300311472|ref|YP_003775564.1| amino acid ABC transporter/sign... 67 1e-12 gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/sign... 64 2e-11 gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/sign... 63 2e-11 >gi|300313642|ref|YP_003777734.1| arogenate dehydratase [Herbaspirillum seropedicae SmR1] Length = 267 Score = 387 bits (993), Expect = e-109, Method: Compositional matrix adjust. Identities = 172/231 (74%), Positives = 204/231 (88%) Query: 30 SRLDEVIKSGKLRVCMTGDYKPFTYFKTDNTFEGMDVDLAQSLAKSLGVEVQLVKTTWTN 89 SRLD+VIK+GKLR+CMTGDYKPFTY++ D +FEGMDV+L Q+LAKSLGVE Q +KTTW+N Sbjct: 36 SRLDQVIKAGKLRICMTGDYKPFTYYRPDQSFEGMDVELGQALAKSLGVEAQFIKTTWSN 95 Query: 90 LMTDFLAKCDIAMGGVSVTLDRQKKAAFAVSHMVDGKSPIVRCADVAKFQTLEMIDKPTT 149 LM DF+A+CDIAMGGVS+TLDR +KAAF+ MVDGK+PI+RCAD KF+ +MID+P T Sbjct: 96 LMNDFIAQCDIAMGGVSITLDRARKAAFSEPTMVDGKAPIIRCADKDKFRNFDMIDQPGT 155 Query: 150 RAIFNPGGTNERFARANYKQAQLILHPDNVTIFQQIIDGKADIMVTDASETLWQAKQHPE 209 RAI NPGGTNERFARA YK+A L LHPDNVTIFQQI+DGKAD+MVTDASETLWQ+K HPE Sbjct: 156 RAIVNPGGTNERFARARYKRATLTLHPDNVTIFQQIVDGKADVMVTDASETLWQSKLHPE 215 Query: 210 LCPVHPDQPLQFSEKAFMLPRADVAFKEYVDAWMHLQKATGDYDRVLNKWL 260 LCPV PDQPLQF+EKA++LPR DVAFK YVD W+HL KATG+Y ++ +KWL Sbjct: 216 LCPVTPDQPLQFAEKAYLLPRGDVAFKAYVDTWLHLAKATGEYQQIFDKWL 266 >gi|300313886|ref|YP_003777978.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 63/250 (25%), Positives = 110/250 (44%), Gaps = 30/250 (12%) Query: 23 TAGAAESSRLDEVIKSGKLRVCMTGDYKPFTYFKTDNTFEGMDVDLAQSLAKSLGVEVQL 82 TA AA + +LD++ K+GK+R+ T F Y G DV+ A+ LA+ LGV++ L Sbjct: 22 TAHAALADQLDDIKKAGKIRIATTSSTPLFGYSDEKLQLAGSDVEAARLLAQDLGVQLDL 81 Query: 83 VKTTWTNLMTDFLA-KCDIAMGGVSVTLDRQK----KAAFAVSHMVDGKSPIVRCADVAK 137 + + A + DI +G +S+T +R K +AV ++ G + D A Sbjct: 82 IPVANAARVPTLQANRADIVVGSLSITPERLKVIDFSTPYAVISLIIGAPKSMVIKDYAD 141 Query: 138 FQTLEMIDKPTTRAIFNPGGTNERFARANYKQAQLILHPDNVTIFQQIIDGKADIMVTDA 197 + TRA N+ N K A+++ + D+ T+ ++ G+ D+ + Sbjct: 142 LNGKRI---GVTRAT-----PNDTLTTQNAKGAEIMRYEDDATLITSMVTGQVDVFSSTP 193 Query: 198 SETLWQAKQHPELCPVHPDQPLQFSEKAFML--------PRADVAFKEYVDAWMHLQKAT 249 S K+ P + ++F +KAF L PR KE++D W+ Sbjct: 194 SNLQEMQKKAP-----GKNLEMKFEQKAFDLGIAINKNQPR----LKEWIDGWVKTNMKN 244 Query: 250 GDYDRVLNKW 259 G + + K+ Sbjct: 245 GKLNAIYKKY 254 >gi|300311472|ref|YP_003775564.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 67.4 bits (163), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 66/264 (25%), Positives = 114/264 (43%), Gaps = 12/264 (4%) Query: 1 MKKYFRKWLLPLTLLCAGMAMQTAGAAESSRLDEVIKSGKLRVCMTGDYKPFTYFKTDNT 60 M K ++WLL + A + + + + L V SG L+V + G+Y PF FK T Sbjct: 1 MNKNIKQWLL--AGVGAALLASSLSVSAADLLQSVKSSGTLKVALEGNYPPFN-FKDPKT 57 Query: 61 FE--GMDVDLAQSLAKSLGVEVQLVKTTWTNLMTDFLA-KCDIAMGGVSVTLDRQKKAAF 117 E G +VD+A+ LA LGV+ T W+ ++ A K D+ + V +T +RQK F Sbjct: 58 GELTGFEVDVAKLLAAKLGVKPVFTTTEWSGILAGLGAGKYDVIINQVGITDERQKAFDF 117 Query: 118 AVSHMVDGKSPIVRCADVAKFQTLEMIDKPTTRAIFNPGGTNERFARANYKQAQLILHPD 177 + + + IVR + +F++LE D + G E+ A+A + +P Sbjct: 118 SDPYTLSSAQLIVRKDEKREFKSLE--DLKGKKLGLGQGTNFEQKAKA-VPGIDVRTYPG 174 Query: 178 NVTIFQQIIDGKADIMVTDASETLWQAKQHPELCPVHPDQPLQFSEK-AFMLPRADVAFK 236 + + G+ D + D+ + K P+ P+ +K + + FK Sbjct: 175 SPEYLADLAAGRIDAALNDSLLVGYILKSTN--LPLKAGSPIGAVDKIGIPFRKGNPEFK 232 Query: 237 EYVDAWMHLQKATGDYDRVLNKWL 260 ++ + KA G + KW Sbjct: 233 AALNKALADIKADGSFKAASEKWF 256 >gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 63.5 bits (153), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 61/263 (23%), Positives = 115/263 (43%), Gaps = 12/263 (4%) Query: 1 MKKYFRKWLLPLTLLCAGMAMQTAGAAESSRLDEVIKSGKLRVCMTGDYKPFTYFKTDNT 60 M+ RK +L + L G+A G A + L ++ K+G +R+ + D+ PF TD Sbjct: 1 MQMSPRKTMLAVVL---GLAAMQGGLARADALADIQKNGVVRIGVPQDFAPFGSVNTDLQ 57 Query: 61 FEGMDVDLAQSLAKSLGVEVQLVKTTWTNLMTDFLA-KCDIAMGGVSVTLDRQKKAAFAV 119 +G+D+D+A+ +A+ +GV++QLV N + K D+ + + +R+K F+ Sbjct: 58 LQGLDIDVARLIAQKMGVKLQLVPVASANRIAYLQTHKADLVISTLGRNAEREKVIDFSQ 117 Query: 120 SHMVDGKSPIVRCADVAKFQTLEMIDKP--TTRAIFNPGGTNERFARANYKQAQLILHPD 177 + S + A V ++ DK R F + + K A + + D Sbjct: 118 PYAPYNNS-VFGVASVKVSGPADLADKTVGVARGTFQ----DLQLTDTAPKSATIKRYED 172 Query: 178 NVTIFQQIIDGKADIMVTDASETLWQAKQHPELCPVHPDQPLQFSEKAFMLPRADVAFKE 237 N + + G+ ++ T A++ P PV +Q S L + + A Sbjct: 173 NNAMISAYVSGQVQLVGTGDFVAYALAEKAPNNKPVL-KYIIQESACNVGLNKGEPALLA 231 Query: 238 YVDAWMHLQKATGDYDRVLNKWL 260 V+ + K +G+ + ++ KWL Sbjct: 232 KVNEALTAAKKSGELNGIVQKWL 254 >gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 63.2 bits (152), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 57/251 (22%), Positives = 107/251 (42%), Gaps = 13/251 (5%) Query: 15 LCAGMAMQTAGAAESSRLDEVIKSGKLRVCMTGDYKPFTYFKTDNTFEGMDVDLAQSLAK 74 L AG M +A A + LD++ K G LRV + D+ PF D +G+D+D+A +AK Sbjct: 10 LMAGAMMFSASVARADALDDIQKHGTLRVAVPADFPPFGSVDADLKPQGLDIDVATLIAK 69 Query: 75 SLGVEVQLVKTTWTNLMTDFLA-KCDIAMGGVSVTLDRQKKAAFAVSH--MVDGKSPIVR 131 LGV+V+L+ + N + K D+ + + +R+K F+ ++ +G + Sbjct: 70 KLGVKVELIPVSSANRIPYLTTKKVDLVISSMGKNAEREKVIDFSAAYAPFFNG---VFG 126 Query: 132 CADVAKFQTLEMIDKPTTRAIFNPGGTNERFARANYKQAQLILHPDNVTIFQQIIDGKAD 191 AD++ ++ K T A+ + + A + + DN + + G+ Sbjct: 127 PADLSVKSAADLAGK--TIAVTRGSVEDLELTKIVPASATVKRYEDNNSTISSFLSGQVQ 184 Query: 192 IMVTDASETLWQAKQHPELCPVHPDQPLQFSEKA--FMLPRADVAFKEYVDAWMHLQKAT 249 ++ T ++P P P+ + L + + ++ VDA + K Sbjct: 185 LVATGNVVAAAIIARNP---PKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAESKKD 241 Query: 250 GDYDRVLNKWL 260 G + KWL Sbjct: 242 GSLSAISQKWL 252 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 0.322 0.134 0.407 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: 807,367 Number of extensions: 30149 Number of successful extensions: 100 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 100 Number of HSP's successfully gapped: 9 Length of query: 261 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 178 Effective length of database: 1,226,865 Effective search space: 218381970 Effective search space used: 218381970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 129 (54.3 bits)