Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate GFF4197 Psest_4270 TRAP transporter, DctM subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__psRCH2:GFF4197 Length = 426 Score = 333 bits (854), Expect = 6e-96 Identities = 176/426 (41%), Positives = 266/426 (62%), Gaps = 3/426 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAW-WIDIPLQAMMIQVASGVNKFSLLAIP 59 M L + VL+ IG+PVA +LGL+ + + ++++ I++ ++LLAIP Sbjct: 1 MTILFLFAALFVLMFIGVPVAVSLGLAGSLTIMIFSQDSVRSLAIKLFETSEHYTLLAIP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAGA M GG++RRL+ FA VG +RGGL++ ++A F A+SGSS A A+VGS Sbjct: 61 FFLLAGAFMTTGGVARRLIDFANACVGHIRGGLAIGAVLACMLFAALSGSSPATVAAVGS 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 + I M R GYP+ F + + +L PPS V+Y AA S+ LFMAG++PG Sbjct: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSVVMVVY--AAATETSVGKLFMAGVVPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 +LL +M I A K+N P RE L A +A+WGL+ MVIILGGI SG+FT T Sbjct: 179 ILLGGALMIAIYIIAVKKNLPALPRASFREWLSAARKAIWGLLLMVIILGGIYSGMFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+AAVA V+S FV +F+Y+D RD PK++ + + ++M +I A F +V+T QIP Sbjct: 239 EAAAVAAVYSAFVALFVYKDISLRDCPKVLLESGKLSIMLMFIIANAMLFAHVLTTEQIP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 IT + ++ L+ +N +L++ G M+ + +ILIL PIL P+ +G+DP+H G Sbjct: 299 QAITAWVIEAGLQPWMFLLVVNIVLLIAGAFMEPSAIILILAPILFPIAIQLGIDPIHLG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 +IM+VN+ IGLITPPVG LFV SA+ + + ++A++P+ + L+ +TY+P+ISL Sbjct: 359 IIMVVNMEIGLITPPVGLNLFVASAVTGMPVTQVIRAVLPWLALMLSFLVIITYVPSISL 418 Query: 420 WLPSVV 425 LP+++ Sbjct: 419 ALPNML 424 Lambda K H 0.329 0.142 0.418 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: 564 Number of extensions: 24 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: 426 Length of database: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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: 51 (24.3 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