Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_1139 PP_1139 branched chain amino acid transporter - permease subunit
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Putida:PP_1139 Length = 418 Score = 356 bits (914), Expect = e-103 Identities = 218/446 (48%), Positives = 279/446 (62%), Gaps = 42/446 (9%) Query: 16 VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAI-FVAVAAIGRFAMV 74 + + L +A F+A+L + + +GLK +I ++V G I +AV ++ F V Sbjct: 1 MNRNLKQAFFSALLVWAVAFPVLGLKL--SIDGISLVVHSQGSFTISIIAVCSVLMFLRV 58 Query: 75 VFIRP-------NIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKG 127 +F + DR+ + A L + + + ++ ++VVA+ Sbjct: 59 LFDKQWSSVMGRRSDRKLIPPAVSNYLTLPKTQRY-------------VIIGLIVVALVW 105 Query: 128 PQ-GSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGL 186 P GS VD ILIYV+L GLNIVVGLAGLLDLGYV FYAVGAYSYA+LS Y G Sbjct: 106 PFFGSRGAVD-IATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYAMLSHYLGW 164 Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGI 246 SFWV LP++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD T G GI Sbjct: 165 SFWVCLPIAGLMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDWTGGPNGI 224 Query: 247 SSIPKATLFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLR 302 S+IPK FG+ F+ A + FH L +S IFL+ + L L +L +V RL Sbjct: 225 SNIPKPEFFGLTFERRAAEGMQTFHEFFGLQYNSINKVIFLYLVALLLALLALFVINRLL 284 Query: 303 RMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFV 362 RMPIGRAWEALREDEIACR+LG+N KL+AF GA FAGFAGSFFAARQG V+PESF Sbjct: 285 RMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFT 344 Query: 363 FLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIF 422 F+ESA+ILAIVVLGGMGS G+ +AAIVM+ EL+RE S YRML+F Sbjct: 345 FIESAIILAIVVLGGMGSQLGVILAAIVMILLPELMREFS-------------EYRMLMF 391 Query: 423 GLAMVVVMLFKPRGFVGSREPTAFLR 448 G MV++M+++P+G + + P LR Sbjct: 392 GALMVLMMIWRPQGLLPMQRPHMELR 417 Lambda K H 0.330 0.145 0.432 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: 630 Number of extensions: 46 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 418 Length adjustment: 32 Effective length of query: 431 Effective length of database: 386 Effective search space: 166366 Effective search space used: 166366 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: 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