Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_010629602.1 BZY95_RS02765 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_002151265.1:WP_010629602.1 Length = 295 Score = 142 bits (359), Expect = 7e-39 Identities = 97/295 (32%), Positives = 151/295 (51%), Gaps = 17/295 (5%) Query: 4 FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63 F+ QLL GL G+ Y L+++G +++G++ ++NFAHG ++MLG FA L+ L Sbjct: 12 FMGQLLLGLINGAFYALLSLGLAVIFGLLKIVNFAHGAMYMLGAFATLLGMRYL------ 65 Query: 64 LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSI----TLSNFI 119 + L++A L L IERV R + L L+ G+++ TL NF Sbjct: 66 ---GINYWAALLLAPLFVGLLGMLIERVLLRRIGHLDHLYGLLLTFGLALIFEGTLVNFF 122 Query: 120 QVTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 V+ G R P P + YQ G + + + +++ V+ WYI+ RT LG RA Sbjct: 123 GVS-GAR-YPTPEALQGGYQTGFMFLPKYRAWVLLAALVVCFATWYIIERTRLGAYLRAG 180 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 ++ + GVNV +++T+ G ALAA AG + Y V S G + F V Sbjct: 181 TENPALMQAFGVNVPLLVTLTYGFGVALAAFAGVLAAPLYPV-SPTMGSNLLIVVFAVVV 239 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 +GG+GS+ GA+ GL +GLIE L Y+ A V F ++ VL+ +P G+ G+ Sbjct: 240 IGGMGSILGAIVTGLAMGLIEGLTKVYYPEAANTV-IFLVMILVLLLRPAGLFGK 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: 319 Number of extensions: 19 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: 300 Length of database: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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 24 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