Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3280 PS417_16790 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__WCS417:GFF3280 Length = 293 Score = 123 bits (309), Expect = 4e-33 Identities = 91/305 (29%), Positives = 154/305 (50%), Gaps = 17/305 (5%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M +F + LL GL G++Y LVAIG+ ++Y G+ NFA G + + FAAL F+ L Sbjct: 1 MTFFFETLLGGLLAGTMYSLVAIGFVLIYKASGVFNFAQGSMLL---FAAL-TFVSLHD- 55 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 G+P A+ LLV ++V ++ L IER+ RPL ++ + +G+S + Q Sbjct: 56 -QGVPFALALLVTVIVMIVGALL----IERLVLRPLVNRSQITLFMATLGLSFIIEGLAQ 110 Query: 121 VTQGPRNKPIPPMVSSVYQF-GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 G + + + + V F G + +S +I VL+T+ + N+T +G + RA Sbjct: 111 GLMGSQVRALDLGIDDVPLFVGPLMLSQFDLIAAAAAVVLVTVLALLFNKTRIGVSLRAV 170 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 D A +G+N+++ I + + + VAG ++ GV F+ +KA + Sbjct: 171 ADDTTAALSIGINLNRIWQIVWAVAGIVGLVAGLLWGARQGV-QFSLSLVV-LKALPVLI 228 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYF--TIAYKDVATFA-ILAFVLIF-KPTGILGRP 295 +GG S+ GA+ GGL++G E+L Y I FA +LA ++ +P G+ G Sbjct: 229 IGGFTSIGGAIVGGLIVGAAENLAEVYIGPLIGGGITPWFAYVLALAFLYIRPAGLFGER 288 Query: 296 EVEKV 300 +E+V Sbjct: 289 AIERV 293 Lambda K H 0.329 0.143 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: 293 Number of extensions: 20 Number of successful extensions: 5 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: 300 Length of database: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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: 48 (23.1 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