Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_083529437.1 AS188_RS12245 ATP-binding cassette domain-containing protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_001482365.1:WP_083529437.1 Length = 313 Score = 110 bits (274), Expect = 4e-29 Identities = 66/222 (29%), Positives = 109/222 (49%), Gaps = 7/222 (3%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+ +GL A+GG V+ V F V G + +G+NGAGKTTTM+ +TG L G + + Sbjct: 22 VLEARGLSRAFGGRTVVEDVSFRVEPGRMTGFVGANGAGKTTTMRMLTGVLRTTAGEVLW 81 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENL-QMGAYIRKDKAGILADIEKMFT 127 G+ + + G +PE RG++ R + + L +G D+ LA+ ++ Sbjct: 82 DGRPVTAAD-----RAGFGYMPEERGLYPRQPVLDQLCYLGRLHGMDRRAALAEARRLLE 136 Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187 +D L GT+S G QQ + + AL+ P L+LDEP GL P+ VD + ++R+ Sbjct: 137 RLDLAGRERDPL-GTLSLGNQQRVQIAAALLHGPTALVLDEPFSGLDPVAVDAMTGLLRE 195 Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQL 229 GV ++ + D V+ +G + G + L Sbjct: 196 RLEQGVPVLFSSHQLDLVDRLCDSLVVLSAGRVLAAGAVEDL 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: 170 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: 313 Length adjustment: 25 Effective length of query: 217 Effective length of database: 288 Effective search space: 62496 Effective search space used: 62496 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