Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate 8500478 DvMF_1227 carbon starvation protein CstA (RefSeq)
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Miya:8500478 Length = 603 Score = 522 bits (1345), Expect = e-152 Identities = 272/602 (45%), Positives = 390/602 (64%), Gaps = 44/602 (7%) Query: 34 ISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDPTRATPAVINNDGLNYVPTNRYVLFGH 93 ++AL +V A++ V+ +AYR+Y L++ + V+ + P R TPAV DG +YV TN+YVLFGH Sbjct: 1 MNALTLVFAALCVFAIAYRFYGLFLTRTVLGVKPGRPTPAVRMADGHDYVETNKYVLFGH 60 Query: 94 HFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVVLAGAVQDFMVLFISSRRNGASLGEMI 153 HFAAIA AGPL+GPVLAAQ GYLPGTLW+L G V+AGAV D +VLF S R G SL + Sbjct: 61 HFAAIAAAGPLLGPVLAAQFGYLPGTLWILVGCVVAGAVHDTVVLFASVRHKGQSLAYIA 120 Query: 154 KEEMGPVPGTIALFGCFLIMIIILAVLALIVVKALAESPWGVFTVCSTVPIALFMGIYMR 213 +E+ G++A F I+I+ LA L++ VV A+ +S WG FTV +T+PIAL MG+Y+ Sbjct: 121 SKEIDKFTGSVASFAVLFILILTLAGLSIAVVNAMHDSAWGTFTVFATIPIALLMGVYLH 180 Query: 214 FIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYWGPALTFKDTTITFALIGYAFVSALLP 273 R G V S+IG+VLL +I G + P TI ++ Y F +++LP Sbjct: 181 VWRDGDVKGASIIGVVLLALAILAGPYVVEHPVLSSWFNMSRHTIALSIPVYGFAASVLP 240 Query: 274 VWLILAPRDYLATFLKIGVIVGLALGIVVLNPELKMPAMTQYIDGTGPLWKGALFPFLFI 333 VWL+L PRDYL+T+LKIG I LA+GI ++P L+M A+T +++G GP+ GA+FPFLFI Sbjct: 241 VWLLLCPRDYLSTYLKIGTIAALAVGIFWVHPTLQMEAITPFVNGGGPIIPGAVFPFLFI 300 Query: 334 TIACGAVSGFHALISSGTTPKLLANETDARFIGYGAMLMESFVAIMALVAASIIEPGLYF 393 TIACGA+SGFHA+I++GTTPK++ NE D F+GYGAML E FVAIMAL+AA ++ P YF Sbjct: 301 TIACGALSGFHAIIATGTTPKMIGNERDLLFVGYGAMLTEGFVAIMALIAACVLVPADYF 360 Query: 394 AMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDVTAHAAATVSSWGFVISPEQILQTAKD 453 A+N+ PA + A+L ++P + A+ Sbjct: 361 AINSAPA-------------------VYAKLG----------------MTPVDLPHLAQA 385 Query: 454 IGEPSVLNRAGGAPTLAVGIAHVFHKVLPMAD-MGFWYHFGILFEALFILTALDAGTRSG 512 +GE ++ R GGA +LAVG+AH+F + M M +WYHF I+FEA+FILTA+D GTR G Sbjct: 386 VGE-NIQGRPGGAVSLAVGMAHIFSSIPFMEHLMSYWYHFAIMFEAVFILTAVDTGTRVG 444 Query: 513 RFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGLWGYLLYQGVVDPLGGVKSLWPLFGIS 572 RF LQ+++G +P + + +I +A WGYL+Y G + ++WPLFG+S Sbjct: 445 RFFLQEMIGTVVPKFAEKRWMPGILITSALFTASWGYLVY------TGDISTIWPLFGMS 498 Query: 573 NQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVWLLICTTWALGLKLFSTNPQMEGFFYM 632 NQ+LAAV L++GT ++I+M + +Y W+T +P + +++ T WA L + + N +G + + Sbjct: 499 NQLLAAVGLLIGTTMIIRMNKAKYAWMTAIPGLSMVVITFWAGYLNVMN-NYLPKGLYLL 557 Query: 633 AS 634 +S Sbjct: 558 SS 559 Lambda K H 0.327 0.142 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1155 Number of extensions: 63 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 716 Length of database: 603 Length adjustment: 38 Effective length of query: 678 Effective length of database: 565 Effective search space: 383070 Effective search space used: 383070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory