Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013135595.1 ARNIT_RS08945 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000092245.1:WP_013135595.1 Length = 240 Score = 238 bits (607), Expect = 8e-68 Identities = 121/240 (50%), Positives = 172/240 (71%), Gaps = 6/240 (2%) Query: 5 SNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDG 64 +N++LL+V+ L V+YG I A+KG++ V GE+V+++G+NGAGKTTT++ I+G L G Sbjct: 3 NNEILLEVRDLHVSYGAISAIKGINLTVLRGEVVTILGANGAGKTTTLRTISGLLKPKSG 62 Query: 65 NIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK--DKAGILADI 122 NI + I A D+V G+ PEGR VF +T+ ENL MGAY K DK + Sbjct: 63 NIIFDKNDITKSEAHDIVTLGMSHSPEGRRVFGTLTVEENLMMGAYTLKGYDKE----TL 118 Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIF 182 + ++ I PRL+ERK QLAGT+SGGEQQMLA+GRA+MS+PK+L+LDEPS+GL+PI++ IF Sbjct: 119 DWIYDILPRLKERKKQLAGTLSGGEQQMLAIGRAIMSKPKLLILDEPSLGLAPILIKAIF 178 Query: 183 EVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242 + ++++ GVT++LVEQNA AL +ADR YV+E G IT G ++LLN ++ AYLG+ Sbjct: 179 KAIKEIALNGVTVLLVEQNAKAALKLADRAYVLEVGKITHEGTAEELLNSKTIQEAYLGK 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: 173 Number of extensions: 8 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: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 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