Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_011840944.1 RSPH17029_RS06705 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_000015985.1:WP_011840944.1 Length = 267 Score = 110 bits (276), Expect = 3e-29 Identities = 68/233 (29%), Positives = 121/233 (51%), Gaps = 9/233 (3%) Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212 P + TF NY +L DP+ G + N+LT + T I I VA AAYA + F G Sbjct: 43 PHDLTFQNYRTILTDPSWYMG----YVNSLTYVVLNTAISITVALPAAYAFSRYRFLGDK 98 Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272 L ++ + P + +P L++++G+ ++ LAH F +PLA+++L +M G+ Sbjct: 99 HLFFWLLTNRMAPPAVFALPFFQLYSSVGLFDTHIAVALAHCLFNVPLAVWILEGFMSGV 158 Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFL-IDATGQ 331 P++I E A +DG + + F KI +PL + A F F+++W +LL+++ ++A Sbjct: 159 PKEIDETAYIDGYSFPRFFVKIFMPLIASGIGVAAFFCFMFSWVELLLSRTLTSVNAKPI 218 Query: 332 TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSV 384 MT + G +W +LA A +++ LV + ++ ++ +G G V Sbjct: 219 AATMTRTV----SASGLDWGVLAAAGVLTLIPGGLVIWFVRNYIAKGFALGRV 267 Lambda K H 0.323 0.138 0.419 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: 274 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: 385 Length of database: 267 Length adjustment: 28 Effective length of query: 357 Effective length of database: 239 Effective search space: 85323 Effective search space used: 85323 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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