Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_092349198.1 BLU87_RS12685 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_900107645.1:WP_092349198.1 Length = 318 Score = 205 bits (521), Expect = 2e-57 Identities = 118/340 (34%), Positives = 196/340 (57%), Gaps = 47/340 (13%) Query: 10 IGAVALLVLPLILQSFGNA-WVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68 +G A L++ +L + N+ W +A L++ ++AL +I++G AG+ ++G F+ +GA Sbjct: 7 LGFPAFLIIMAVLPNMLNSRWQAVAITFLIFTVVALSQDIILGKAGMFNMGQALFFGMGA 66 Query: 69 YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128 Y+ A++ S + + + IPVA +L A FG +L P + LRGDYL Sbjct: 67 YITAILNSQY----------------GWPILVTIPVAIILPALFGVLLSGPIIHLRGDYL 110 Query: 129 AIVTLGFGEI-IRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVT 187 +VT+GF + +++ NNL +T GP G+ +DS+ +FG L +L V Sbjct: 111 LVVTIGFNIVFVQVVQNNLG---GITGGPNGIFGLDSISIFGKQLTDQLSV--------- 158 Query: 188 LYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASF 247 YY+ F+VL++ ++ I L+ S++GRA +RED++AA+++GINTR K+ AF +GA Sbjct: 159 -YYFAFVVLLI-TLGIMRNLEKSKVGRALHYLREDQLAAESIGINTRIYKIFAFALGAGI 216 Query: 248 GGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYV 307 G++G +F A VSPE+F ++SV+ ++V++GG IPGV+LG ++ LPE+ R Sbjct: 217 AGLAGTVFAAQYSAVSPEAFEFIQSVLFFSIVLVGG-SSIPGVLLGVFVMFVLPEIFR-- 273 Query: 308 AGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPS 347 + A R + AMI+ M+LRPRG+WP+ Sbjct: 274 ------------EFATWRFFIFGFAMILAMILRPRGIWPA 301 Lambda K H 0.328 0.144 0.430 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: 302 Number of extensions: 17 Number of successful extensions: 6 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: 358 Length of database: 318 Length adjustment: 28 Effective length of query: 330 Effective length of database: 290 Effective search space: 95700 Effective search space used: 95700 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 (21.7 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