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= 0029.0238.p (189 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspir... 387 e-109 gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspir... 202 1e-53 gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [... 131 3e-32 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 102 1e-23 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 93 1e-20 >gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 250 Score = 387 bits (993), Expect = e-109, Method: Compositional matrix adjust. Identities = 189/189 (100%), Positives = 189/189 (100%) Query: 1 MSLLGHNGAKQSGPAAVQPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRLTWLA 60 MSLLGHNGAKQSGPAAVQPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRLTWLA Sbjct: 62 MSLLGHNGAKQSGPAAVQPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRLTWLA 121 Query: 61 SELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASKDARF 120 SELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASKDARF Sbjct: 122 SELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASKDARF 181 Query: 121 ANNPMVTSAPFIRFYAAVPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALATDMMA 180 ANNPMVTSAPFIRFYAAVPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALATDMMA Sbjct: 182 ANNPMVTSAPFIRFYAAVPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALATDMMA 241 Query: 181 LQLMELQQH 189 LQLMELQQH Sbjct: 242 LQLMELQQH 250 >gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 236 Score = 202 bits (514), Expect = 1e-53, Method: Compositional matrix adjust. Identities = 98/189 (51%), Positives = 130/189 (68%), Gaps = 9/189 (4%) Query: 1 MSLLGHNG----AKQSGPAAVQPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRL 56 MSL+GH ++ GP ++ A A +E +A + + + + RF RL Sbjct: 51 MSLIGHQEVPAVGEEDGPEELEALAYP-----AGAEEGDRAAFVERIIERSAPDTRFDRL 105 Query: 57 TWLASELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASK 116 TWLASELL+ PI+L+TF T+ELQIF +AHGL++ TPR+WAFCNY E VF V+D Sbjct: 106 TWLASELLDAPISLITFLTSELQIFKSAHGLSLNETPRAWAFCNYTIAHEGVFAVSDTQT 165 Query: 117 DARFANNPMVTSAPFIRFYAAVPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALAT 176 D RF NNP+VTS PF RFYA V LMY+GKAFGSLC+IDTE R+LRS E++AL+ELA LA+ Sbjct: 166 DMRFMNNPLVTSTPFFRFYAGVRLMYEGKAFGSLCVIDTEPRILRSHEQQALEELAMLAS 225 Query: 177 DMMALQLME 185 D++ L ++E Sbjct: 226 DILRLHILE 234 >gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 131 bits (330), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 65/143 (45%), Positives = 93/143 (65%), Gaps = 1/143 (0%) Query: 48 QAEARFHRLTWLASELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDED 107 Q+E RF RL WLASELL+VP++L+ +E I+H GL++ T R AF + + E Sbjct: 2 QSEERFRRLNWLASELLDVPMSLIGLVASETVIWHGPVGLHVEETTRPCAFVEHTLLHEG 61 Query: 108 VFTVADASKDARFANNPMVTSAPFIRFYAAVPL-MYQGKAFGSLCIIDTEARLLRSQERR 166 VF V DASKD RF+++ +VT APF+R +A + L + G FG+LC++DTE R+ R++E R Sbjct: 62 VFLVPDASKDPRFSDHSLVTGAPFVRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIR 121 Query: 167 ALQELAALATDMMALQLMELQQH 189 + LA +A D+ L L E Q H Sbjct: 122 TFEGLAQIAEDIYRLFLFERQSH 144 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 102 bits (255), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 57/130 (43%), Positives = 77/130 (59%), Gaps = 2/130 (1%) Query: 47 TQAEARFHRLTWLASELLEVPIALVTFQTAELQIFHAAHGLNIAA-TPRSWAFCNYADMD 105 T E RF RLT LA L +VP+A+VT Q F + GL A T R +FC +A + Sbjct: 25 TPREERFDRLTRLARRLFDVPMAVVTMIDVNRQWFKSCVGLGDATETSREVSFCAHAILH 84 Query: 106 EDVFTVADASKDARFANNPMVTSAPFIRFYAAVPLMYQ-GKAFGSLCIIDTEARLLRSQE 164 E++ V DA+ D RF+ NP VT PFIRFYA P+ + G G+LC++DT R + E Sbjct: 85 EEMTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADE 144 Query: 165 RRALQELAAL 174 R L++LAA+ Sbjct: 145 RALLKDLAAM 154 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 93.2 bits (230), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 55/134 (41%), Positives = 75/134 (55%), Gaps = 2/134 (1%) Query: 27 EAASTDEA-RQAPLMAQAKTGTQAEARFHRLTWLASELLEVPIALVTFQTAELQIFHAAH 85 EAA E+ R A L T + ++T LA + +V IALV Q F + Sbjct: 12 EAAVRQESQRLAQLHGYCALDTPPDKLCDQVTQLACSMFDVEIALVALVDEHRQWFKSRV 71 Query: 86 GLNIAATPRSWAFCNYADMDEDVFTVADASKDARFANNPMVTSAPFIRFYAAVPLMY-QG 144 GL ++ TPR+ +FCN+A V DA +DARF+ + +VT APFIRFYA PL+ QG Sbjct: 72 GLEVSETPRADSFCNHAIQTRHGMVVTDALQDARFSRHALVTGAPFIRFYAGAPLVTPQG 131 Query: 145 KAFGSLCIIDTEAR 158 + G+LCIID+ R Sbjct: 132 LSLGTLCIIDSRPR 145 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 0.320 0.128 0.368 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: 454,544 Number of extensions: 15012 Number of successful extensions: 51 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 46 Number of HSP's successfully gapped: 7 Length of query: 189 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 109 Effective length of database: 1,241,070 Effective search space: 135276630 Effective search space used: 135276630 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: 128 (53.9 bits)