Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012760292.1 RLEG_RS30575 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000023185.1:WP_012760292.1 Length = 239 Score = 187 bits (476), Expect = 1e-52 Identities = 102/233 (43%), Positives = 149/233 (63%), Gaps = 3/233 (1%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 LL+ +GL +YGG QA+ GVD V GE V++IG+NGAGKTT M++I+G L+ +I Y Sbjct: 3 LLETRGLTASYGGFQALFGVDIVVGAGETVAIIGANGAGKTTLMRSISGVLTNAASSILY 62 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 + I A D++ G+ MVPEGR +F +++ ENL +G Y RK +E +F + Sbjct: 63 RDEPIGALSAPDILARGIAMVPEGRKLFPSLSVEENLLVGNYGRKVDGPWT--LESIFAL 120 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 FP L+ER+D A +SGG+QQM+A+GR LMS P +LL DE S+GL+P++V I+ + Sbjct: 121 FPILKERRDNPATALSGGQQQMVAIGRGLMSNPAMLLCDEISLGLAPVVVRDIYAAFPRI 180 Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 G +IV+VEQ+ ++AL +ADR Y M G +T++G L D + AY G Sbjct: 181 RETGASIVIVEQDIAQALKVADRVYCMMEGRVTLSGRAADLSRD-DIHKAYFG 232 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: 169 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: 239 Length adjustment: 23 Effective length of query: 219 Effective length of database: 216 Effective search space: 47304 Effective search space used: 47304 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 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