Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_086510095.1 BZY95_RS11670 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_002151265.1:WP_086510095.1 Length = 280 Score = 108 bits (269), Expect = 2e-28 Identities = 73/237 (30%), Positives = 120/237 (50%), Gaps = 12/237 (5%) Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212 P T ANY + + +A FN++ V I +L+ A+YAL + F GR Sbjct: 51 PTRATLANYAQIF----SQRSFLQAIFNSILVATSVVFIALLLGITASYALGRVRFRGRT 106 Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272 ++ +I+G+ + P L L + A+ + G L++T F +P +++L +M L Sbjct: 107 SVLLIILGVSMFPQVAVLSGLFEVIRALNLYNNPGGLILSYTIFTLPFTVWVLTTFMRQL 166 Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQT 332 P ++ E A +DGAT + TK+ LPL +PA+A+ + F+ WN+ L A F + + +T Sbjct: 167 PLELEEAAIMDGATPWVTITKVFLPLMWPAMATTGLLAFIAAWNEFLFALTFTLTDSQRT 226 Query: 333 TVMTNQIVELLGTRGGNWEI---LATAAFVSIAVPLLVF-FSMQRFLVRGLLAGSVK 385 + L + G +E+ AA V + VPL+V QR +V GL AG+VK Sbjct: 227 V----PVAIALLSGGSAYELPWAPIMAASVVVTVPLVVLVIIFQRRIVSGLTAGAVK 279 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: 237 Number of extensions: 13 Number of successful extensions: 1 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: 280 Length adjustment: 28 Effective length of query: 357 Effective length of database: 252 Effective search space: 89964 Effective search space used: 89964 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: 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