Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate H281DRAFT_01744 H281DRAFT_01744 TRAP transporter, DctM subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Burk376:H281DRAFT_01744 Length = 631 Score = 243 bits (621), Expect = 9e-69 Identities = 137/415 (33%), Positives = 225/415 (54%), Gaps = 3/415 (0%) Query: 14 MFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFLLSGAFMTTGG 73 + +GVPI L S L L + + ++ ++H+ LLAIPFF+L+G M T G Sbjct: 218 LVLGVPIGFVLAFSALLYFLADPSLPMLVYSQQVMAGTDHFVLLAIPFFVLAGLLMETNG 277 Query: 74 VARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAIAGMVRSGYPQ 133 ++ RLI+ G +RGGL + ++A F+ +SGS A +AAVG + + + +S Sbjct: 278 MSSRLIELLLRIFGRVRGGLGLITIMATAFFSGVSGSKLADIAAVGGVVMPAVRQSKEDP 337 Query: 134 AFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGLILMVVIYIVA 193 A ++ + + IPP + M++ S+ LF+AGVVP +L + L +V I Sbjct: 338 NEAAALLACSAVMAETIPPCVNMIIMGFVANISIAGLFLAGVVPAAVLAVALAIVAVIFG 397 Query: 194 RVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAVAAVYSAFVAL 253 R L A + R W+ AL L+++ +I G+ SG T TE +A A VY+ V Sbjct: 398 RRINL-ADALTNPRAWMPLLGGALVALVMITMIGKGVTSGIATSTEVSAFAVVYALIVGW 456 Query: 254 FVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIASWVTELG--LS 311 +R++ +V + S + ++FI+A A + LT EQIP ++ + Sbjct: 457 LAFRELTPKSVARVFVRSASMASSILFIVAAASSVSFALTIEQIPALVSDSMIAFAHQYG 516 Query: 312 PWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVVNMEIGLIT 371 P MFLL+ +++++ G +E + ++I P+ PIA +LGI+P+H G ++VV M +GL Sbjct: 517 PTMFLLLSVLIMIVFGAVLEGAPALIIFGPLLTPIATQLGINPLHFGTVIVVAMGLGLFA 576 Query: 372 PPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPNWLGM 426 PPVGL LF T A+TG + A R L +L++L + L+++ +P+ SL LP LG+ Sbjct: 577 PPVGLGLFATCAITGTEMKAVARPMLKYLLVLCIALVVLVLVPSFSLWLPTRLGL 631 Score = 36.2 bits (82), Expect = 3e-06 Identities = 47/185 (25%), Positives = 79/185 (42%), Gaps = 24/185 (12%) Query: 69 MTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAAL----SGSSPATVAAVGSIAIA 124 + G V + ANA G + + ++ C+L AA + S PA GS+ IA Sbjct: 155 LVIGSVFMTIFALANAVNGARK--TVLGTLIGCLLLAAAVFAWNASVPAHAIKPGSLLIA 212 Query: 125 GMVRS---GYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLL 181 G V + G P F ++ + L L PS+ M+VY+ F+ +P +L Sbjct: 213 GFVGALVLGVPIGF---VLAFSALLYFLADPSLPMLVYSQQVMAGTDH-FVLLAIPFFVL 268 Query: 182 GLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 +LM + +R+ +L L + GL L+ I+ +SG + ++ A Sbjct: 269 AGLLMETNGMSSRLIEL----------LLRIFGRVRGGLGLITIMATAFFSGV-SGSKLA 317 Query: 242 AVAAV 246 +AAV Sbjct: 318 DIAAV 322 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: 669 Number of extensions: 40 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: 2 Length of query: 427 Length of database: 631 Length adjustment: 35 Effective length of query: 392 Effective length of database: 596 Effective search space: 233632 Effective search space used: 233632 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