Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__Miya:8502075 Length = 243 Score = 285 bits (728), Expect = 8e-82 Identities = 140/241 (58%), Positives = 184/241 (76%), Gaps = 1/241 (0%) Query: 20 LIRIEGLNKHYGA-FHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQ 78 +I+ + ++K Y + HVL+DI L++++GE +V+CGPSGSGKSTLIRCIN+LE Q+G I Sbjct: 1 MIKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIV 60 Query: 79 VDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARM 138 VDG+D+ +R+++G VFQ FNL+PHM+VL+N LAP VR R +AE+ A Sbjct: 61 VDGVDINDPRTNLTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKTAME 120 Query: 139 YLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVL 198 L KV I +A YP QLSGGQQQRVAIAR L MKPRIMLFDEPTSALDPEM+ EVLDV+ Sbjct: 121 LLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVM 180 Query: 199 VQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQI 258 QLA GMTM+CVTHEMGFAR+VA+RV+F++ G ++E++ P+ FF+ P +R K FL++I Sbjct: 181 RQLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFLSKI 240 Query: 259 L 259 L Sbjct: 241 L 241 Lambda K H 0.322 0.137 0.395 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: 219 Number of extensions: 5 Number of successful extensions: 1 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: 260 Length of database: 243 Length adjustment: 24 Effective length of query: 236 Effective length of database: 219 Effective search space: 51684 Effective search space used: 51684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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