Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_4865 PP_4865 High-affinity branched-chain amino acid transport system permease protein BraE
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Putida:PP_4865 Length = 435 Score = 315 bits (808), Expect = 1e-90 Identities = 191/427 (44%), Positives = 252/427 (59%), Gaps = 29/427 (6%) Query: 16 VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVV 75 +++ L E + A +L+ +F VG+ D N W V +GRF + + Sbjct: 19 LKRSLLETIVAGLLALIVFGPVVGVVLDGYTFNAEPRRVAW-----LVGGVMVGRFLLSL 73 Query: 76 FIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKGPQGSLTYV 135 F++ +R L G + + + ++ ++V+AI P + Y+ Sbjct: 74 FLQTAPGQRMLLGFDSGGSGVHVTAPDYKSR------LRYIIPALIVIAIVFPIFANKYL 127 Query: 136 DNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLS 195 I LIYV+L GLNIVVGLAGLLDLGYVAFYA+GAY AL Y GL FW +LPL+ Sbjct: 128 LTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWSVLPLA 187 Query: 196 GIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF 255 I AAL G ILGFPVLR+ GDYLAIVTL FGEIIRLVL NW T G G+ + P T F Sbjct: 188 AIAAALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGMPA-PSPTFF 246 Query: 256 GIPFDATA--GG--FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWE 311 G+ F A GG + F +++ +F++ ++ + + Y+ RL RMP+GRAWE Sbjct: 247 GLEFGRRAKDGGVPIHEFFGFEYNASLKFVFIYAVLFMVVLAVLYIKHRLTRMPVGRAWE 306 Query: 312 ALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILA 371 ALREDEIACRS+G+N V KL+AF GA AG AG FFA QGFV+P SF F ESA+ILA Sbjct: 307 ALREDEIACRSMGLNHVLVKLSAFTLGASTAGLAGVFFATYQGFVNPSSFTFFESALILA 366 Query: 372 IVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVML 431 IVVLGGMGS G+ IAA V+ ELLR S YR+L+FG+ MV++M+ Sbjct: 367 IVVLGGMGSTVGVVIAAFVLTVAPELLRSFS-------------EYRVLLFGVLMVLMMI 413 Query: 432 FKPRGFV 438 ++PRG + Sbjct: 414 WRPRGLI 420 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: 650 Number of extensions: 35 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: 435 Length adjustment: 33 Effective length of query: 430 Effective length of database: 402 Effective search space: 172860 Effective search space used: 172860 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