Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate RR42_RS10605 RR42_RS10605 C4-dicarboxylate ABC transporter permease
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Cup4G11:RR42_RS10605 Length = 615 Score = 235 bits (600), Expect = 2e-66 Identities = 141/423 (33%), Positives = 229/423 (54%), Gaps = 19/423 (4%) Query: 14 MFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFLLSGAFMTTGG 73 + +GVPI L + L L + + ++ ++H+ LLAIPFF+L+G M G Sbjct: 202 LVLGVPIGFVLAFAALLYFLADPSLPMLVYSQQVMAGTDHFVLLAIPFFVLAGLLMEANG 261 Query: 74 VARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAIAGMVRSGYPQ 133 ++ RLI+ G +RGGL + ++A F+ +SGS A VAAVG I + + R+ Sbjct: 262 MSSRLIELLLRVFGRVRGGLGLITIIATAFFSGVSGSKLADVAAVGGIVMPAVRRTRQDP 321 Query: 134 AFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGLILMVVIYIVA 193 AG++ + + IPP I +++ S+ LF+AG+VP ++ L L V+ IV Sbjct: 322 GEAAGLLACSAVMAETIPPCINLILMGFVANISIAGLFMAGLVPAAVMALSLAVLAVIVG 381 Query: 194 RVKKLPAMPRVSLREWLASARKALWGLL-------LMVIILG-GIYSGAFTPTEAAAVAA 245 R +++ E R LW LL +MV ++G G+ SG T TE +A A Sbjct: 382 R--------KINPDEAFEH-RTPLWPLLGGALVALIMVGMIGKGVTSGIATSTEVSAFAV 432 Query: 246 VYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIASWV 305 VY+ V +R++ L ++ + S + ++FI+A A + LT EQIPQ ++ + Sbjct: 433 VYALVVGGLAFRELNLRSVARLFVRSASMAGGILFIVAAASSVSFALTIEQIPQLMSGTM 492 Query: 306 TELGLS--PWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363 T MF+++ +++++ G +E + ++I P+ PIA +LG++P+H G +MV+ Sbjct: 493 TAFAAQYGSVMFIMLSALLMMVFGAVLEGAPALIIFGPLLTPIAQQLGVNPLHFGTVMVI 552 Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPNW 423 M +GL PPVGL LF T A+TG + R L +L +LLV L+++ +PA SL LPN Sbjct: 553 AMGLGLFAPPVGLGLFATCAITGTQVKDVARPMLKYLAVLLVALVLLILVPAFSLWLPNR 612 Query: 424 LGM 426 LGM Sbjct: 613 LGM 615 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: 682 Number of extensions: 41 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: 427 Length of database: 615 Length adjustment: 35 Effective length of query: 392 Effective length of database: 580 Effective search space: 227360 Effective search space used: 227360 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: 52 (24.6 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