Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_038203065.1 Q392_RS06000 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000745855.1:WP_038203065.1 Length = 240 Score = 238 bits (606), Expect = 1e-67 Identities = 120/241 (49%), Positives = 172/241 (71%), Gaps = 2/241 (0%) Query: 1 MAEKSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLS 60 M + ++ +LQV L+ YG I+A+ GV + GELV+L+G+NGAGKTT ++ I+G L Sbjct: 1 MDKDASPPVLQVSDLRAGYGRIEALHGVSLRLGAGELVALVGANGAGKTTLLRTISGLLP 60 Query: 61 MNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILA 120 G +E+LG+ + V+ GL V EGR VF +++ +NL++GA++ +D A Sbjct: 61 ARAGRVEFLGQDVTRAAPDQRVRRGLAQVLEGRQVFGPLSVEDNLRLGAFVHRDAAE--E 118 Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180 + +M+ +FP L E+KD AGT+SGG+QQMLAM RALMS PKVLLLDEPSMGL+P++V + Sbjct: 119 RMRRMYRLFPVLEEKKDLPAGTLSGGQQQMLAMARALMSGPKVLLLDEPSMGLAPLLVRE 178 Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 +F VVR++ G+ I+LVEQNA ALAIADRGYV+E+G +T+ GP + L +D +VR+AYL Sbjct: 179 VFRVVRELKEQGIPILLVEQNARAALAIADRGYVLETGKVTLEGPARALQDDERVRSAYL 238 Query: 241 G 241 G Sbjct: 239 G 239 Lambda K H 0.317 0.136 0.373 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: 184 Number of extensions: 5 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: 242 Length of database: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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