Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012467210.1 CLIM_RS11655 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000020465.1:WP_012467210.1 Length = 328 Score = 85.1 bits (209), Expect = 2e-21 Identities = 73/242 (30%), Positives = 113/242 (46%), Gaps = 27/242 (11%) Query: 10 LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69 ++ KGL+ +G ++AV+GVD EV GEL +G NGAGKTT M +TG + G+IE Sbjct: 9 IRAKGLEKRFGDVRAVQGVDIEVAPGELFGFLGPNGAGKTTAMTMLTGLSRPDAGSIEIG 68 Query: 70 GK--SIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYI-------RKDKAGILA 120 G S K A L+ +VP+ ++ ++ ENL + R+ KA L Sbjct: 69 GVDCSKNPKAAQHLIG----VVPDESNLYPELSGFENLCFSGALYGMRRDERRRKASELL 124 Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGL----SPI 176 D+ L + + S G ++ L + A+M P +L LDEP+ G+ SP Sbjct: 125 DLFD-------LGDAASRKFSGYSKGMKRRLVIAAAIMHDPPLLFLDEPTSGIDVASSPY 177 Query: 177 MVDKIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVR 236 + D++ GVTI + A + DR + +G I T ++LL + R Sbjct: 178 DTP---HCLSDLHRNGVTIFMTTHFIDEAERLCDRIAFIVNGRIVRTDTVERLLQPVQGR 234 Query: 237 AA 238 A Sbjct: 235 YA 236 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: 178 Number of extensions: 9 Number of successful extensions: 3 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: 328 Length adjustment: 26 Effective length of query: 216 Effective length of database: 302 Effective search space: 65232 Effective search space used: 65232 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 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