Align Carbon starvation protein A (characterized, see rationale)
to candidate 8500478 DvMF_1227 carbon starvation protein CstA (RefSeq)
Query= uniprot:A0A0C4Y7X7 (690 letters) >FitnessBrowser__Miya:8500478 Length = 603 Score = 567 bits (1461), Expect = e-166 Identities = 295/562 (52%), Positives = 381/562 (67%), Gaps = 20/562 (3%) Query: 32 VSALWIVVAAICIYLIAYRYYSKFIAEKVMQLDPKRMTPAWRHNDGLDYVPTNKAVLFGH 91 ++AL +V AA+C++ IAYR+Y F+ V+ + P R TPA R DG DYV TNK VLFGH Sbjct: 1 MNALTLVFAALCVFAIAYRFYGLFLTRTVLGVKPGRPTPAVRMADGHDYVETNKYVLFGH 60 Query: 92 HFAAIAGAGPLVGPVLAAQMGYMPGMLWILAGVVFAGAVQDFMVLFISTRRDGRSLGDLI 151 HFAAIA AGPL+GPVLAAQ GY+PG LWIL G V AGAV D +VLF S R G+SL + Sbjct: 61 HFAAIAAAGPLLGPVLAAQFGYLPGTLWILVGCVVAGAVHDTVVLFASVRHKGQSLAYIA 120 Query: 152 KSEMGTVPGMIALFGCFMIMIIILAVLALIVVKALAGSPWGTFTVGVTIPIALFMGIYTR 211 E+ G +A F I+I+ LA L++ VV A+ S WGTFTV TIPIAL MG+Y Sbjct: 121 SKEIDKFTGSVASFAVLFILILTLAGLSIAVVNAMHDSAWGTFTVFATIPIALLMGVYLH 180 Query: 212 YIRPGRIGEVSVIGFVLLMLAIIGGQYVHESAVLAPLFTYDGKALTWMLIIYGFIAAVLP 271 R G + S+IG VLL LAI+ G YV E VL+ F + + +YGF A+VLP Sbjct: 181 VWRDGDVKGASIIGVVLLALAILAGPYVVEHPVLSSWFNMSRHTIALSIPVYGFAASVLP 240 Query: 272 VWLLLAPRDYLSTFLKIGTIIALAIGILIVAPELKMPAFTQFAKGGGPVWSGNLFPFLFI 331 VWLLL PRDYLST+LKIGTI ALA+GI V P L+M A T F GGGP+ G +FPFLFI Sbjct: 241 VWLLLCPRDYLSTYLKIGTIAALAVGIFWVHPTLQMEAITPFVNGGGPIIPGAVFPFLFI 300 Query: 332 TIACGAVSGFHALISSGTTPKLLESEAHMRFIGYGAMLAESFVAIMALVAASVIEPGVYF 391 TIACGA+SGFHA+I++GTTPK++ +E + F+GYGAML E FVAIMAL+AA V+ P YF Sbjct: 301 TIACGALSGFHAIIATGTTPKMIGNERDLLFVGYGAMLTEGFVAIMALIAACVLVPADYF 360 Query: 392 AMNSPAAVIGTSPESVAQVVSGWGFVITPDVLIQTAKDVGENSIISRAGGAPTLAVGIAH 451 A+NS AV +TP L A+ VGEN I R GGA +LAVG+AH Sbjct: 361 AINSAPAVYAK-------------LGMTPVDLPHLAQAVGEN-IQGRPGGAVSLAVGMAH 406 Query: 452 ILHQVVGGQAMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPSFRRTDSLP 511 I + + +M++WYHFAI+FEA+FILTAVD GTR GRF LQ+++G+ VP F +P Sbjct: 407 IFSSIPFMEHLMSYWYHFAIMFEAVFILTAVDTGTRVGRFFLQEMIGTVVPKFAEKRWMP 466 Query: 512 ANLIATALTVSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVLGTCVLVKMKRG 571 LI +AL + WGY +Y G I+T+WPLFG+SNQ+LAAV L++GT ++++M + Sbjct: 467 GILITSALFTASWGYLVY------TGDISTIWPLFGMSNQLLAAVGLLIGTTMIIRMNKA 520 Query: 572 QYAWVTLVPTIWLLICTLTAGW 593 +YAW+T +P + +++ T AG+ Sbjct: 521 KYAWMTAIPGLSMVVITFWAGY 542 Lambda K H 0.328 0.141 0.437 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: 1148 Number of extensions: 51 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 690 Length of database: 603 Length adjustment: 38 Effective length of query: 652 Effective length of database: 565 Effective search space: 368380 Effective search space used: 368380 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 (21.8 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