Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_3578 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3578 Length = 426 Score = 318 bits (816), Expect = 2e-91 Identities = 193/427 (45%), Positives = 254/427 (59%), Gaps = 29/427 (6%) Query: 16 VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVV 75 +++ + +A+ A ++S +F VG+ D N W VA+ IGRFA+ + Sbjct: 10 IKQSVIDAILAGLISLIVFGPIVGVVLDGYSFNLQPARVGW-----LVAIVMIGRFALSL 64 Query: 76 FIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKGPQGSLTYV 135 F++ + L + + + ++ ++V+AI P + YV Sbjct: 65 FLQTPKGLKILQGFESTGSGVHVLPPDYKSR------LRWIIPALIVIAIVFPFFANKYV 118 Query: 136 DNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLS 195 I LIYV+L GLNIVVGLAGLLDLGYVAFYA+GAY AL Y GL FW +LPL+ Sbjct: 119 LTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLA 178 Query: 196 GIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF 255 I AA+ G ILGFPVLR+ GDYLAIVTL FGEIIRLVL NW T G G+ +P T Sbjct: 179 AIAAAMAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM-PVPSPTFL 237 Query: 256 GIPFDATA--GG--FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWE 311 G+ F A GG F + F + + +F++ ++ +L YV RL RMP+GRAWE Sbjct: 238 GLEFGRRAKDGGVPFHEFFGIDYNPNIKFLFIYIVLFITVLLVLYVKHRLTRMPVGRAWE 297 Query: 312 ALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILA 371 ALREDEIACRS+G+N V KL+AF GA AG AG FFA+ QGFV+P SF F ESA+ILA Sbjct: 298 ALREDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILA 357 Query: 372 IVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVML 431 IVVLGGMGS G+ IAA V+ ELLR S YR+L+FG+ MV++M+ Sbjct: 358 IVVLGGMGSTVGVVIAAFVLTVAPELLRSFS-------------EYRVLLFGVLMVLMMI 404 Query: 432 FKPRGFV 438 ++PRG + Sbjct: 405 WRPRGLI 411 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: 636 Number of extensions: 39 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 431 Effective length of database: 394 Effective search space: 169814 Effective search space used: 169814 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