Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028585878.1 G494_RS0119635 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000429965.1:WP_028585878.1 Length = 310 Score = 259 bits (663), Expect = 5e-74 Identities = 150/346 (43%), Positives = 203/346 (58%), Gaps = 48/346 (13%) Query: 2 KNTKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYV 61 +N T +I A +VLPL+ ++ + I A YV+L LGLNIVVGYAGLLDLGY Sbjct: 10 RNRITILMILAGMAMVLPLVANNYV---LEILTNAWFYVVLCLGLNIVVGYAGLLDLGYA 66 Query: 62 AFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTL 121 AF+AVGAY ++ S + W+ IPVA + + G ++G PTL Sbjct: 67 AFFAVGAYTTGILTSE----------------FGVNFWLTIPVAVVASMITGVIIGGPTL 110 Query: 122 KLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGF 181 +LR DYLAIVTLGFGEI+RI NL+ +T G GL I+ +FGL L Sbjct: 111 RLRSDYLAIVTLGFGEIVRICARNLE----ITGGASGLIGIERPSLFGLHL--------- 157 Query: 182 DINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAF 241 N + +YY+FL L +++ I YRLQ SR+GRAW +REDE AA+AMGI +KL A+ Sbjct: 158 --NQINHFYYVFLALAILACFISYRLQHSRLGRAWQYVREDEDAAEAMGIGRVAIKLYAY 215 Query: 242 GMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALP 301 +GA FGGV+G F A +SPE+F +SV+I+ VVLGG+G IPGV++GA L P Sbjct: 216 VIGAIFGGVAGCFFAAKMTAISPETFMFQQSVLILVGVVLGGMGKIPGVVIGAFALVLFP 275 Query: 302 EVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPS 347 EV R + +R L+ A+ M++I+L RP G+WP+ Sbjct: 276 EVFRGIGS--------------MRMLVFAVVMLVIILYRPEGIWPA 307 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: 356 Number of extensions: 14 Number of successful extensions: 5 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: 310 Length adjustment: 28 Effective length of query: 330 Effective length of database: 282 Effective search space: 93060 Effective search space used: 93060 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