Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_028585879.1 G494_RS0119640 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000429965.1:WP_028585879.1 Length = 304 Score = 239 bits (611), Expect = 4e-68 Identities = 132/303 (43%), Positives = 196/303 (64%), Gaps = 5/303 (1%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 ++ +QQL NGL LGS Y LVA+GYTMVYGII ++NFAHGD++M G F + FL L S Sbjct: 4 LDILLQQLANGLILGSFYALVALGYTMVYGIIKLLNFAHGDLYMCGAFIGFL-FLSLVSG 62 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 G +L M +++M+ L I+RVAY P+ + RL+ LITA+ +S+ LSN + Sbjct: 63 LLGESWGGILCSM-ILSMITVGLLGVLIQRVAYLPMLAAPRLSILITALAVSMVLSNGVM 121 Query: 121 -VTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 +T G + + GN+ V+ QI ++V A+L+ ++ +NRT G+A RA Sbjct: 122 ALTDGEYEAFSTDLGFEGLEMGNVFVTYTQIALVVSAALLMVTLFFFINRTMYGKAMRAI 181 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 D+ L+G+NV++ I++TF +G+ALAA AG M +YYG F GF G+KAFTAAV Sbjct: 182 AIDQDACRLMGINVNKVITLTFFIGSALAAAAGVMAGVYYGSVHFFMGFVIGLKAFTAAV 241 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWS--AYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297 +GGIGS+ GA+ GGL++GL+E+ + + +KDV +F IL +L+FKPTG+LG+ E+ Sbjct: 242 IGGIGSIRGAMLGGLVLGLLEAFGTQIPFIGSEWKDVFSFGILILLLVFKPTGLLGKTEI 301 Query: 298 EKV 300 E++ Sbjct: 302 ERM 304 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: 318 Number of extensions: 21 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: 304 Length adjustment: 27 Effective length of query: 273 Effective length of database: 277 Effective search space: 75621 Effective search space used: 75621 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