Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS22325 AZOBR_RS22325 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__azobra:AZOBR_RS22325 Length = 286 Score = 218 bits (556), Expect = 8e-62 Identities = 117/240 (48%), Positives = 167/240 (69%), Gaps = 9/240 (3%) Query: 9 LLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDG--- 64 LL V ++V Y + V +G+ EV EGE+V+L+G+NGAGK+TT+KAI+G L DG Sbjct: 27 LLSVNNIEVVYNDVILVLRGLSLEVPEGEIVALLGANGAGKSTTLKAISGLLKTEDGEVT 86 Query: 65 --NIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADI 122 +I + G+ I G +V+ G+ V EGR + MT ENL++GA+ R+D G+ DI Sbjct: 87 RGDISFAGERINGIDPDKIVRRGIFQVMEGRRIIGDMTCQENLRLGAFTRRD-GGVKDDI 145 Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIF 182 E ++ FPRL+ER LAG +SGGEQQMLA+GRA+M++PK++L+DEPSMGLSP+MV ++F Sbjct: 146 EMVYHYFPRLKERTG-LAGYLSGGEQQMLAIGRAMMARPKLILMDEPSMGLSPLMVKEVF 204 Query: 183 EVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 ++R + LGVTI+LVEQNA AL A RGY+ME+G + + G ++L N+ V+ YLG Sbjct: 205 SIIRQINKDLGVTILLVEQNARMALQAATRGYIMENGKVVLDGTAEELRNNEDVKEFYLG 264 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: 199 Number of extensions: 10 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: 242 Length of database: 286 Length adjustment: 25 Effective length of query: 217 Effective length of database: 261 Effective search space: 56637 Effective search space used: 56637 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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