Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= uniprot:Q88GX2 (236 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 103 bits (258), Expect = 3e-27 Identities = 70/211 (33%), Positives = 116/211 (54%), Gaps = 5/211 (2%) Query: 26 GLLVTAKLVAISFSLGAVLGLLLALARLSRSLVLQRMAAGYVYFFRGSPLLAQLFLLYYG 85 G+ +T + +F+ VLGL+LA+A LSR L+ +++A Y RG P++ L + + Sbjct: 43 GIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFA 102 Query: 86 L-GSLKGFWQDVGL-WWFFRDAWFCT--LLAFTLNTAAYQAEIFRGSLMAVAPGQHEAAR 141 L ++ W +GL RD +LA L AA+ AE+FR L++V GQ EAA+ Sbjct: 103 LVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQIEAAK 162 Query: 142 ALNLKRSTTFFKVILPQSLLVAIGPLGNELILMIKASAIASLVTIYDLMGVTKLAFSRSF 201 AL L F +I PQ+ + PLGN+ + M+K S++ S++ + D+ + K+ + +F Sbjct: 163 ALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTAAGNF 222 Query: 202 D-FQIYLWAAVLYLVIVELVRRLLKHLEARL 231 F+ Y A++YL + + L+ LEA L Sbjct: 223 RYFETYNVVALIYLAMTVTLSLALRKLEAHL 253 Lambda K H 0.331 0.144 0.433 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: 124 Number of extensions: 7 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: 236 Length of database: 262 Length adjustment: 24 Effective length of query: 212 Effective length of database: 238 Effective search space: 50456 Effective search space used: 50456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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