Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate RR42_RS10605 RR42_RS10605 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS10605 Length = 615 Score = 239 bits (611), Expect = 1e-67 Identities = 142/426 (33%), Positives = 237/426 (55%), Gaps = 14/426 (3%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMI---QVASGVNKFSLLAIPFF 61 +L FI +++G+P+ + L +AL+ +++ P M++ QV +G + F LLAIPFF Sbjct: 193 LLAIGFIGALVLGVPIGFVLAFAALL--YFLADPSLPMLVYSQQVMAGTDHFVLLAIPFF 250 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 VLAG +M GMS RL+ + G VRGGL L+ I+A+ FF +SGS +AD A+VG ++ Sbjct: 251 VLAGLLMEANGMSSRLIELLLRVFGRVRGGLGLITIIATAFFSGVSGSKLADVAAVGGIV 310 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 +P + R + + +V A PP N +L A +SIA LFMAG++P + Sbjct: 311 MPAVRRTRQDPGEAAGLLACSAVMAETIPPCINLILMGFVA--NISIAGLFMAGLVPAAV 368 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREAL-KIAGEALWGLMAMVIILGGILSGVFTATE 240 ++ + L +I +K N E R L + G AL L+ + +I G+ SG+ T+TE Sbjct: 369 MALSLAVLAVIVGRKIN--PDEAFEHRTPLWPLLGGALVALIMVGMIGKGVTSGIATSTE 426 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP- 299 +A AVV++ V +R+ R + +L R+ ++ ++ A+S + +T+ QIP Sbjct: 427 VSAFAVVYALVVGGLAFRELNLRSVARLFVRSASMAGGILFIVAAASSVSFALTIEQIPQ 486 Query: 300 --SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVH 357 S TAF + +M ++M+ G V++ AP ++I P+L P+ +GV+P+H Sbjct: 487 LMSGTMTAF-AAQYGSVMFIMLSALLMMVFGAVLEGAPALIIFGPLLTPIAQQLGVNPLH 545 Query: 358 FGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAI 417 FG +M++ +G+GL PPVG LF AI ++ + ++ + L + L+ + +PA Sbjct: 546 FGTVMVIAMGLGLFAPPVGLGLFATCAITGTQVKDVARPMLKYLAVLLVALVLLILVPAF 605 Query: 418 SLWLPS 423 SLWLP+ Sbjct: 606 SLWLPN 611 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: 770 Number of extensions: 41 Number of successful extensions: 4 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: 615 Length adjustment: 35 Effective length of query: 391 Effective length of database: 580 Effective search space: 226780 Effective search space used: 226780 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: 52 (24.6 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