Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate BWI76_RS24135 BWI76_RS24135 c4-dicarboxylate permease
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Koxy:BWI76_RS24135 Length = 433 Score = 318 bits (816), Expect = 2e-91 Identities = 170/426 (39%), Positives = 270/426 (63%), Gaps = 3/426 (0%) Query: 4 LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAI--KLFETSEHYTLLAIPF 61 L LF F+L+FIGVPI+ S+G++ ++LL P + + + +L +++ LLAIPF Sbjct: 7 LMLFGSFFILVFIGVPISFSIGIATVGSMLLMFPWDIAVITVSQRLANGLDNFALLAIPF 66 Query: 62 FLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSI 121 F+ +G M +GG+A RLI+ A VG + G L VLA M+F ++SGS+ A AAVG Sbjct: 67 FIFAGTLMNSGGIAIRLINLAQVMVGRVPGSLGHVNVLANMMFGSISGSAVAAAAAVGGT 126 Query: 122 AIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYA-AATETSVGKLFIAGVVPGLL 180 R GY AF + ++ G+LIPPS V++V++ A SV LF+AG +PG+L Sbjct: 127 LNPIQTRKGYDPAFSTAVNVSSCITGLLIPPSNVLIVFSLTAGGVSVASLFMAGYLPGIL 186 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 +GL +MVV I+A+ + P R + + + AL LLL++I++GGI G FT TEA Sbjct: 187 MGLAIMVVCAIIAKRRGYPVSERPTCAQAAKAFFDALPSLLLVIIVMGGILGGIFTATEA 246 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 +A+A VY+ +++ +YR+++ + PK++LES +T +++ +I ++ + +T IP Sbjct: 247 SAIAVVYTFILSVLIYREVKWRDLPKLILESVVMTSIVLLLIGFSVGMSWAMTNADIPYM 306 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 I+ + + +P + LL++NIVLLI G FM+ + +LI PIF PIA +LG+DP+H GI+ Sbjct: 307 ISDALMGISENPVVILLLINIVLLIVGIFMDMTPAVLIFTPIFLPIAQDLGMDPVHFGIM 366 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 MV N+ IGL+TPPVG LFV +++G+ + I+ LP+ LL+ L+++ YIP +SL + Sbjct: 367 MVANLCIGLLTPPVGSALFVGCSISGVKIQQLIKPLLPFYAALLIALMMIVYIPQISLFI 426 Query: 421 PNWLGM 426 P LG+ Sbjct: 427 PQLLGL 432 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: 514 Number of extensions: 30 Number of successful extensions: 4 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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