Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_005454736.1 SACCYDRAFT_RS06670 ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >NCBI__GCF_000244975.1:WP_005454736.1 Length = 338 Score = 152 bits (383), Expect = 2e-41 Identities = 95/297 (31%), Positives = 162/297 (54%), Gaps = 5/297 (1%) Query: 71 ILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDLSVGAV 130 +L A+L + +FF+I+ Y + IL + + L+IG + VI TGGIDLS+G Sbjct: 31 LLAFASLIVIYAFFSIASPYFFTYDNFTAILFSTVVIGTLAIGTTFVIITGGIDLSIGTG 90 Query: 131 MAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLLMVAGR 190 MA+ + L+ + L + ++ G L G +NG ++FL I P +ATL +M+ Sbjct: 91 MALCAVMSGVFLVDLGLPLPLGVLCAVLFGGLVGLVNGLNIAFLKIPPFIATLAMMLVAE 150 Query: 191 GVAQLINQGQIITFQH-PGFAAIGVGQFL---GLPMPVWIVIGMLTFSQLLLRKTALGLF 246 G+A +++ I F PG+ + G + P V I+I + + +LL ++ LG + Sbjct: 151 GLALVLSDSAPIYFNDVPGYVELSRGNLIPGVDFPNAVLILIAVAIIASVLLTRSVLGRY 210 Query: 247 IEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWLELDA 306 ++G N +A+ GI+ + K+ Y AGL LAG++ +A + GS G+ EL A Sbjct: 211 TYSIGSNEEATALSGIDVRRWKIAVYAFAGLFIGLAGVLISARL-GSAQPATGMGYELQA 269 Query: 307 VLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTVL 363 + AVVIGG +L+GG+ S++ +++GALII L + + +P ++ +I VIL + Sbjct: 270 IAAVVIGGTSLSGGKGSILGTLIGALIISVLNNGLQIMSIPQEWQNVILGCVILVAV 326 Lambda K H 0.323 0.136 0.379 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: 289 Number of extensions: 15 Number of successful extensions: 2 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: 405 Length of database: 338 Length adjustment: 30 Effective length of query: 375 Effective length of database: 308 Effective search space: 115500 Effective search space used: 115500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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