Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate PP_1167 PP_1167 putative TRAP dicarboxylate transporter, DctM subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Putida:PP_1167 Length = 426 Score = 333 bits (853), Expect = 8e-96 Identities = 179/421 (42%), Positives = 271/421 (64%), Gaps = 6/421 (1%) Query: 7 FLLL---FLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63 F+LL +L+ IG+P+A +LGLS AL + ++++ I++ ++LLAIPFF+ Sbjct: 4 FILLGSFIVLILIGMPVAYALGLS-ALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFV 62 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L+GA M GG++RRL+ FA VG +RGGL++ ++A F A+SGSS A A+VGS+ I Sbjct: 63 LAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLI 122 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVY--AAATETSVGKLFIAGVVPGLLL 181 M R GYP+ F + + +L PPS V+Y AA S+ LF+AG++PGLLL Sbjct: 123 PEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLL 182 Query: 182 GLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 ++M + I A+ + P + LRE L A +ALWGL+ MVIILGGI SG FT TE+A Sbjct: 183 SAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESA 242 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 AVA V+S FV +F+YRD + + PK++ + + ++M +I A F +V+T QIP I Sbjct: 243 AVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKI 302 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIM 361 + L + ++ L+ +N +L++ G M+ + +ILIL PI P+ +G+DP+H G+IM Sbjct: 303 TTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIM 362 Query: 362 VVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421 +VN+ IGLITPPVG LFV SA+ + + +T++A +P+ + L + L+ VTYIPA+SL LP Sbjct: 363 LVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLP 422 Query: 422 N 422 + Sbjct: 423 S 423 Lambda K H 0.330 0.144 0.425 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: 467 Number of extensions: 20 Number of successful extensions: 3 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: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 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 (21.9 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