Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate H281DRAFT_01744 H281DRAFT_01744 TRAP transporter, DctM subunit
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Burk376:H281DRAFT_01744 Length = 631 Score = 228 bits (582), Expect = 3e-64 Identities = 142/460 (30%), Positives = 227/460 (49%), Gaps = 50/460 (10%) Query: 5 LLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLAS-VAGTLFEAFEGHFTLLAIPFF 63 LL + +G L++GVPI L S+ L+ L +D SL V A HF LLAIPFF Sbjct: 209 LLIAGFVGALVLGVPIGFVLAFSALLYFL--ADPSLPMLVYSQQVMAGTDHFVLLAIPFF 266 Query: 64 ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123 +LA M T G++ R+I + G + GGL + + A F+ +SGS A + A+G +V Sbjct: 267 VLAGLLMETNGMSSRLIELLLRIFGRVRGGLGLITIMATAFFSGVSGSKLADIAAVGGVV 326 Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAG 183 + +RQ AA ++ + + IPP + M++ +S+ +FLAGV+P + Sbjct: 327 MPAVRQSKEDPNEAAALLACSAVMAETIPPCVNMIIMGFVANISIAGLFLAGVVPAAVLA 386 Query: 184 LMLMVTIYVMAKVKNLPKG-----EWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTP 238 + L + + + NL W+ A V L++I +I G+ GI T Sbjct: 387 VALAIVAVIFGRRINLADALTNPRAWM------PLLGGALVALVMITMIGKGVTSGIATS 440 Query: 239 TEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHAD 298 TE +A A VYA V +R++ P A Sbjct: 441 TEVSAFAVVYALIVGWLAFRELTPKSVA-------------------------------- 468 Query: 299 TRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAG--FGPVMFLIVVNV 356 + + ++LF++A A + LT EQ+P ++ +M++ +GP MFL++ + Sbjct: 469 --RVFVRSASMASSILFIVAAASSVSFALTIEQIPALVSDSMIAFAHQYGPTMFLLLSVL 526 Query: 357 ILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVT 416 I+++ G +E + L+I PL+ PIA +LGI+P+H G ++VV M +G+ PPVGL LF T Sbjct: 527 IMIVFGAVLEGAPALIIFGPLLTPIATQLGINPLHFGTVIVVAMGLGLFAPPVGLGLFAT 586 Query: 417 SGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 + G M AV R L +L VL + L+++ +P S LP Sbjct: 587 CAITGTEMKAVARPMLKYLLVLCIALVVLVLVPSFSLWLP 626 Score = 35.4 bits (80), Expect = 6e-06 Identities = 47/204 (23%), Positives = 82/204 (40%), Gaps = 19/204 (9%) Query: 64 ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123 ++ S FMT +A + +G L G L +A A + S PA + GS++ Sbjct: 156 VIGSVFMTIFALANAVNGARKTVLGTLIGCLLLAAAVF-----AWNASVPAHAIKPGSLL 210 Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAG 183 IAG V+ + L L PS+ M+VY+ V L + ++AG Sbjct: 211 IAGFVGALVLGVPIGFVLAFSALLYFLADPSLPMLVYSQQVMAGTDHFVLLAIPFFVLAG 270 Query: 184 LMLMVT------IYVMAKVKNLPKGEWLGWGEVAASAANASVG-------LLLIGIILGG 230 L++ I ++ ++ +G LG + A+A + V + G+++ Sbjct: 271 LLMETNGMSSRLIELLLRIFGRVRG-GLGLITIMATAFFSGVSGSKLADIAAVGGVVMPA 329 Query: 231 IYGGIFTPTEAAAVASVYAFFVAT 254 + P EAAA+ + A T Sbjct: 330 VRQSKEDPNEAAALLACSAVMAET 353 Lambda K H 0.329 0.144 0.421 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: 810 Number of extensions: 52 Number of successful extensions: 6 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: 467 Length of database: 631 Length adjustment: 35 Effective length of query: 432 Effective length of database: 596 Effective search space: 257472 Effective search space used: 257472 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 (21.8 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