Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate Echvi_0765 Echvi_0765 Carbon starvation protein, predicted membrane protein
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Cola:Echvi_0765 Length = 544 Score = 221 bits (563), Expect = 7e-62 Identities = 123/351 (35%), Positives = 203/351 (57%), Gaps = 16/351 (4%) Query: 39 IVVASVSVYLVAYRYYSLYIAQKVMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAI 98 +++A++++ + AY Y ++ +K + + TP+ DG++Y P+ V+ GHHFA+I Sbjct: 7 LLLAAITL-IAAYFIYGKFVFKK-FDIRNSHVTPSHKYQDGVDYEPSRPIVVLGHHFASI 64 Query: 99 AGAGPLVGPVLAAQMGYLPGTLWLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMG 158 AGAGP+VGP++A G++P +W+L G + GAV D + S R G S+G +IK+ +G Sbjct: 65 AGAGPIVGPIIAVTFGWIPAVIWILVGGIFFGAVHDLGSMVASLRSEGKSIGTIIKQNIG 124 Query: 159 PVPGTIALFGCFLIMIIILAVLALIVVKALAESPWGVFTVCSTVPIALFMGIYMRFI--R 216 + + F +I+++AV A I+ K +P + +A+ G+ + + R Sbjct: 125 QSGKQLFMLFSFSTLILVIAVFADIIAKTFINNPGVASASILFILLAIVFGLINKMVAHR 184 Query: 217 PGRVGEVSVIGIVLLVASIYFGGVIAHDPYWGPALTFKDTTITFALIGYAFVSALLPVWL 276 SV+G+ L+ +Y G + + L +K + L+ YAF++++ PV L Sbjct: 185 KSLFLLTSVVGVGLMYYFVYLGMQLPFE------LDYK--VWLYVLLAYAFIASVTPVSL 236 Query: 277 ILAPRDYLATFLKIGVIVGLALGIVVLNPELKMPAMTQYIDGTGPLWKGALFPFLFITIA 336 +L PRDYL +FL G+I+ LGI NP++KM G LFP LF+TIA Sbjct: 237 LLQPRDYLNSFLLYGLIIFAVLGIFYANPDIKMDHQIHLASDN----LGYLFPVLFVTIA 292 Query: 337 CGAVSGFHALISSGTTPKLLANETDARFIGYGAMLMESFVAIMALVAASII 387 CGA+SGFH+L++SGTT K + E DA+ +G+G ML+ESF+AI+++ A I+ Sbjct: 293 CGAISGFHSLVASGTTSKQIDKEGDAKIVGFGGMLIESFLAIISVGAVIIL 343 Score = 51.6 bits (122), Expect = 1e-10 Identities = 46/139 (33%), Positives = 66/139 (47%), Gaps = 13/139 (9%) Query: 483 MADMGFWYHFGILFEAL----FILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGII 538 MA +G + F AL F LT LD TR RF Q+ + KT + I Sbjct: 369 MASLGIPEELAVSFVALTVSAFALTTLDTCTRLARFTFQEYFEGAKGPVGKTFASNRYI- 427 Query: 539 GTAGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIW 598 + V + LL GG +LWP+FG +NQ+LAA+AL+ V LIK K + Sbjct: 428 -STSIVVILSILLISS-----GGFTTLWPIFGSANQLLAALALLAVAVWLIK-KNVNATF 480 Query: 599 VTVVPAVWLLICTTWALGL 617 V ++P ++ T +LG+ Sbjct: 481 V-IIPMFFMFTVTLTSLGI 498 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: 919 Number of extensions: 46 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 716 Length of database: 544 Length adjustment: 37 Effective length of query: 679 Effective length of database: 507 Effective search space: 344253 Effective search space used: 344253 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