Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_011383251.1 AMB_RS04130 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000009985.1:WP_011383251.1 Length = 442 Score = 251 bits (641), Expect = 3e-71 Identities = 148/438 (33%), Positives = 238/438 (54%), Gaps = 19/438 (4%) Query: 4 LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKL----FETSEHYTLLAI 59 L F +L L++ + + I +++ L+ L+ + + SL L + +Y L I Sbjct: 8 LTAFGILLLMLVVRIHIGIAMFLAATGIYLVLNHGELNSLLFTLNNLVYARLSNYDLAVI 67 Query: 60 PFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119 P F+L G F T GG+++ L A +GH +GGLA AA AC F A+ GSS AT A +G Sbjct: 68 PLFILMGQFATHGGLSKALFHAAGTLIGHFKGGLAYAATAACAAFGAICGSSLATAATMG 127 Query: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGL 179 +A+ + R Y G + GTLGILIPPS+ +VVYA T+ S+GKLF+A V+PG+ Sbjct: 128 QVALPELTRRNYSGRLATGTLAAGGTLGILIPPSVPLVVYAVLTQESIGKLFVAAVIPGI 187 Query: 180 LLGLILMVVIYIVARV--KKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTP 237 + L M VI I+ + K PA RVSL+E + + + LL+ ++++ GIY G P Sbjct: 188 IAALGYMAVIRIIVSLDPKAGPASERVSLKEMIKAQLGIIPVLLVFLVVIVGIYGGWANP 247 Query: 238 TEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQI 297 TEAA++ A +A+ V MR + + + + T M+ ++ A L L Q+ Sbjct: 248 TEAASIGAAACGIIAV-VSGGMRFKDLKQSVFGTAIATAMIFMVLIGADLLNSALALTQM 306 Query: 298 PQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGID---- 353 P +A+WV G+ P L + + ++ G M+ A+IL+ PIF+P+ LG+D Sbjct: 307 PAELANWVKNSGMPPVAVLFTIIAIYVLLGCVMDSLAMILLTIPIFYPVV--LGLDFYGM 364 Query: 354 -----PIHLGIIMVVNMEIGLITPPVGLNLFVTSAVT-GMPLGATIRAALPWLMILLVFL 407 I GI+ ++ +EIGL+ PPVG+NL+V + + +PL T LP+L + + Sbjct: 365 SVDDKSIWFGIVALMVVEIGLVHPPVGMNLYVINKIAKDVPLKETAMGVLPFLASDFIRI 424 Query: 408 IIVTYIPAVSLALPNWLG 425 +++ + P ++L L + G Sbjct: 425 VVLVFFPPMALWLVHVTG 442 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: 502 Number of extensions: 25 Number of successful extensions: 6 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: 427 Length of database: 442 Length adjustment: 32 Effective length of query: 395 Effective length of database: 410 Effective search space: 161950 Effective search space used: 161950 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