Align TRAP-type large permease component (characterized, see rationale)
to candidate H281DRAFT_01744 H281DRAFT_01744 TRAP transporter, DctM subunit
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_01744 Length = 631 Score = 253 bits (646), Expect = 1e-71 Identities = 139/421 (33%), Positives = 236/421 (56%), Gaps = 4/421 (0%) Query: 5 VFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFIL 64 + I +GA+ +GVP+ F L F ++ + +Q ++AG D F LLAIPFF+L Sbjct: 209 LLIAGFVGALVLGVPIGFVLAFSALLYFLADPSLPMLVYSQQVMAGTDHFVLLAIPFFVL 268 Query: 65 AGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIP 124 AG LM G+S R+I+ + G +RGGLG++ IMA + +SGS AD AA+ +++P Sbjct: 269 AGLLMETNGMSSRLIELLLRIFGRVRGGLGLITIMATAFFSGVSGSKLADIAAVGGVVMP 328 Query: 125 MMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIA 184 + ++ + +A L+A V+A IPP + I+ G AN+SI LF+AG+VP ++ +A Sbjct: 329 AVRQSKEDPNEAAALLACSAVMAETIPPCVNMIIMGFVANISIAGLFLAGVVPAAVLAVA 388 Query: 185 LVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVA 244 L ++ R+ ++ P + + G AL AL M +I G+ +G+ T TE + A Sbjct: 389 LAIVAVIFGRRINLADALTNP-RAWMPLLGGALVALVMITMIGKGVTSGIATSTEVSAFA 447 Query: 245 AVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGF 304 VYAL VG + +REL P+ + V +++A + I+F+V AA S+ +T IP+ ++ Sbjct: 448 VVYALIVGWLAFRELTPKSVARVFVRSASMASSILFIVAAASSVSFALTIEQIPALVSDS 507 Query: 305 ISPLIDR--PTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFI 362 + + PT+ + + +L+++V G L+ P ++I P+L PI Q GI+P++FG + + Sbjct: 508 MIAFAHQYGPTMFLLLSVLIMIVFGAVLEGAPALIIFGPLLTPIATQLGINPLHFGTVIV 567 Query: 363 MNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVI-VPA 421 + +GL PPVG+ L + + V + +L+ + L +LVL P + +P Sbjct: 568 VAMGLGLFAPPVGLGLFATCAITGTEMKAVARPMLKYLLVLCIALVVLVLVPSFSLWLPT 627 Query: 422 R 422 R Sbjct: 628 R 628 Lambda K H 0.331 0.145 0.430 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: 632 Number of extensions: 32 Number of successful extensions: 7 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: 425 Length of database: 631 Length adjustment: 35 Effective length of query: 390 Effective length of database: 596 Effective search space: 232440 Effective search space used: 232440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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