Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_086511812.1 BZY95_RS20875 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_002151265.1:WP_086511812.1 Length = 427 Score = 329 bits (843), Expect = 1e-94 Identities = 176/419 (42%), Positives = 263/419 (62%), Gaps = 4/419 (0%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWID--IPLQAMMIQVASGVNKFSLLAIPFFV 62 +++ + LIL+G+P+A AL + A + L + + + G + F LLAIP FV Sbjct: 5 LMIVGLLGLILMGLPIAVALAIVATVAIVVFQGVEMLPNIGLTMFEGASSFPLLAIPMFV 64 Query: 63 LAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLI 122 LAGAIM GG+S+RL+AFA L GF+RGGL+++NI S FF ISGS+VAD A+ GSVLI Sbjct: 65 LAGAIMNTGGISKRLIAFASALFGFIRGGLAMINIGVSLFFAEISGSAVADVAATGSVLI 124 Query: 123 PEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLL 182 P M+++GYP F+ AVT S + A++ PPS +LY + +G SI LF+AGI+PGLL Sbjct: 125 PAMKKRGYPSSFAAAVTSSSASLAIIIPPSIPMILYGVMSGA--SIVQLFVAGIVPGLLG 182 Query: 183 SAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESA 242 +A +M L +A+K N+P EV + + A EA W L +IILG I G TATE A Sbjct: 183 AAGLMALSYYYARKYNWPVEEVFQFKRVRQTAREAGWALTLPIIILGSIFGGFVTATEGA 242 Query: 243 AVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKI 302 +AV + F++ IYR+ R L K + + ++VM+L+ +A G +T M++P ++ Sbjct: 243 GLAVAAAIFISAVIYRELDLRTLYKAIVDGGQQTAVVMLLVAASALIGVFLTEMRMPQQL 302 Query: 303 TTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIM 362 A L+L+DN+Y ILM +N +L+G + A I+++ PI++P++ G+DPVHFG+++ Sbjct: 303 AQAVLSLTDNKYAILMMLNVFFLLIGLFLHSAAAIILVVPIVMPLVGAAGIDPVHFGLVV 362 Query: 363 LVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421 +NL IG TPPV +VL +I K + S ++ + F L +L+ VTYIPAI + L Sbjct: 363 CLNLAIGQQTPPVASVLITACSIAKSDVWSVTRSNLGFITVLLFILLLVTYIPAIPMAL 421 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: 598 Number of extensions: 21 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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 24 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