Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_011649168.1 RL_RS34925 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_000009265.1:WP_011649168.1 Length = 468 Score = 306 bits (784), Expect = 9e-88 Identities = 168/461 (36%), Positives = 270/461 (58%), Gaps = 45/461 (9%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQ-VASGVNKFSLLAIPFFVL 63 +LLGSF+VL+LIG+PVA ++ +++++ + ++ Q + +GV F LLA+PFF+L Sbjct: 3 LLLGSFLVLMLIGVPVAISMAVASVLYIVLYGVAPDIIVAQRMIAGVESFPLLAVPFFIL 62 Query: 64 AGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIP 123 AG +M G++ R+ +FA LVG+++GGL+ VNI+ S F +SG+++AD A +G++ I Sbjct: 63 AGNLMNSAGVTGRIYSFAVALVGWMKGGLAQVNIIGSVIFSGMSGTALADAAGIGTIEIK 122 Query: 124 EMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLS 183 M+ GYP E + VT + + + PPS V+Y + A VSI +LFMAGI+PG++++ Sbjct: 123 AMKDHGYPVEAAVGVTAASATLGPIFPPSLPFVIYGMMAN--VSIGALFMAGILPGIVMT 180 Query: 184 AVMMGLCLIFAKKRNYPKGEVIPLREALKIAGE--------------------------- 216 +MM FA K+ + +RE L E Sbjct: 181 LLMMITVAAFAYKKRWGSDAPFNVRELLSAGMEIVVVLAVPLAIYLMMRAGVSMNVAAGI 240 Query: 217 ---------------ALWGLMAMVIILGGILSGVFTATESAAVAVVWSFFVTMFIYRDYK 261 A+ LM VI++GG+ G FT TE+A AV+WS F+ + YR Sbjct: 241 ALALLLALDWYFRFSAVMALMTPVILIGGMTMGWFTPTEAAVAAVLWSLFLGLVRYRTMT 300 Query: 262 WRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCIN 321 L K T+ T + V+ ++ A+ F +++T+ Q ++ A L+++DN++V L+ +N Sbjct: 301 PSTLAKASFDTIETTASVLFIVTAASVFAWLLTVSQAAQLLSDAILSITDNKWVFLILVN 360 Query: 322 FMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFV 381 +++ +G +D I IL PILLP++ G+DPV FG+IM +NL IGL+ PP+G VLFV Sbjct: 361 LLMLFVGCFLDTIAAITILVPILLPIVLKFGIDPVQFGLIMTLNLMIGLLHPPLGMVLFV 420 Query: 382 GSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLP 422 S + K+S+E T A++P+ + LFL L+ +T++PAISLWLP Sbjct: 421 LSRVAKLSVERTTMAILPWLVPLFLALILITFVPAISLWLP 461 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: 644 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 468 Length adjustment: 33 Effective length of query: 393 Effective length of database: 435 Effective search space: 170955 Effective search space used: 170955 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