Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Keio:17272 Length = 241 Score = 125 bits (315), Expect = 6e-34 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 3/235 (1%) Query: 10 LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69 L K L AY G + V+ V V GE+V L+G NGAGKTTT + G + + GNI Sbjct: 4 LTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIID 63 Query: 70 GKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD--IEKMFT 127 I + G+ +P+ +F R+++ +NL IR D + + ++ Sbjct: 64 DDDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRANELME 123 Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187 F + +D + ++SGGE++ + + RAL + PK +LLDEP G+ PI V I ++ Sbjct: 124 EF-HIEHLRDSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKRIIEH 182 Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242 + G+ +++ + N LA+ +R Y++ G + G ++L D V+ YLGE Sbjct: 183 LRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYLGE 237 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: 127 Number of extensions: 7 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: 241 Length adjustment: 23 Effective length of query: 219 Effective length of database: 218 Effective search space: 47742 Effective search space used: 47742 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