Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_028320915.1 H567_RS0107410 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000422285.1:WP_028320915.1 Length = 291 Score = 150 bits (380), Expect = 3e-41 Identities = 101/299 (33%), Positives = 160/299 (53%), Gaps = 24/299 (8%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M+ F+Q L+ G+ G +YGL+ +G +++ G++G+IN AHG + M+ + + F L Sbjct: 1 MDVFLQTLVAGILKGGLYGLIGMGMSLIMGVMGIINLAHGQLMMVAMYITFVCFTYL--- 57 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAP---LITAIGMSITLSN 117 GL LL+ + L+ +L I+R A PL L P ++ +G+ + L+ Sbjct: 58 --GLDPYAALLITMPALFLLGAL----IQRYALNPLMEVESLLPENQVLMTVGIGMVLTE 111 Query: 118 FIQVTQGPRNKPIPPMVSSVYQFG---NISVSLKQIIIIVITAVLLT--IFWYIVNRTAL 172 + K + SS F + SV+L I A+L T +FW+++ +T L Sbjct: 112 IARFIFSSDYKSVQTAYSSSSFFLRGISFSVALTAAFFI---ALLFTGFMFWFLL-KTDL 167 Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYL-MYYGVASFNDGFTPG 231 GRA RAT QD+ A L+GV+ + +TF +G+AL A AGT+ + +YY FT Sbjct: 168 GRAIRATAQDKDAALLMGVDAKRITILTFGIGSALVAAAGTLLMPIYYLFPDIGSPFTR- 226 Query: 232 VKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTG 290 KAF +LGG+GS GA+FGGL +GL E+ + Y +A+ D+ I VL+F P+G Sbjct: 227 -KAFVITILGGLGSTVGAIFGGLTLGLAEAFGATYIGMAFDDMIGLLIFILVLLFLPSG 284 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: 285 Number of extensions: 22 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: 300 Length of database: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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 Apr 09 2024. 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