Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_038205678.1 Q392_RS09840 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000745855.1:WP_038205678.1 Length = 239 Score = 235 bits (599), Expect = 7e-67 Identities = 112/237 (47%), Positives = 178/237 (75%), Gaps = 1/237 (0%) Query: 6 NKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN 65 ++++L+++G+ +YG IQA++ V +V G +V+L+GSNGAGK+TT+ A++ + + G Sbjct: 2 SELMLELRGVSASYGAIQALQDVSLKVERGAIVALLGSNGAGKSTTLNAVSHLIEPSAGE 61 Query: 66 IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKM 125 I + G+ I+ + ++V+ GLV VPEGR VF M++ ENL++GA++R+ + + D E++ Sbjct: 62 IFFDGEPIRRCPSDEIVRRGLVQVPEGREVFKDMSVRENLELGAFLRRSRGEVAQDFERV 121 Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185 F FPRL+ER +Q A T+SGGEQQMLA+GRALM++P+++LLDEPSMGLSP++V++IFE + Sbjct: 122 FETFPRLKERSEQKASTLSGGEQQMLAIGRALMARPRMILLDEPSMGLSPLLVEQIFETI 181 Query: 186 RDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 + + G+TI+LVEQ+ AL +A Y++E+G +++ GP QL+NDP VR AYLG Sbjct: 182 QRLNREQGLTILLVEQDVRLALRMARYAYILENGEMSLEGPSSQLMNDPAVRRAYLG 238 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: 177 Number of extensions: 5 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