Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Btheta:353166 Length = 218 Score = 91.3 bits (225), Expect = 1e-23 Identities = 66/217 (30%), Positives = 111/217 (51%), Gaps = 7/217 (3%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMND-GNIE 67 +++++G+ ++G +Q +KG+D E+ +GE+VS++G +GAGKTT ++ I GTL D G + Sbjct: 1 MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQ-IMGTLDEPDAGTVA 59 Query: 68 YLG---KSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEK 124 G +K K + + V + + T EN+ + A+I + + Sbjct: 60 IDGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAM 119 Query: 125 MFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEV 184 F L +R +SGGE+Q +A+ RAL++ P V+L DEPS L + + ++ Sbjct: 120 EILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQL 179 Query: 185 VRDVY-ALGVTIVLVEQNASRALAIADRGYVMESGLI 220 D+ LG T V+V + A I DR M G I Sbjct: 180 FFDLRDRLGQTFVIVTHDEGLA-KITDRTVHMVDGTI 215 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: 120 Number of extensions: 6 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: 218 Length adjustment: 23 Effective length of query: 219 Effective length of database: 195 Effective search space: 42705 Effective search space used: 42705 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 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