Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012116024.1 XAUT_RS20500 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000017645.1:WP_012116024.1 Length = 240 Score = 229 bits (583), Expect = 5e-65 Identities = 116/237 (48%), Positives = 165/237 (69%), Gaps = 4/237 (1%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+V L YG ++ + G+ V+EG+LV+LIGSNGAGKTTT++A++G + G++ Sbjct: 1 MLEVTDLVAGYGKVKVLHGLSLTVQEGQLVTLIGSNGAGKTTTLRAVSGMIVPESGSVRL 60 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR----KDKAGILADIEK 124 G+ + G A+ + K+GL PEGR VF ++ +NL +GA+ R + + + AD+++ Sbjct: 61 DGEDLTGLPAFKITKKGLAHSPEGRRVFPTQSVLDNLLLGAFPRLTGARPRGDVEADLDR 120 Query: 125 MFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEV 184 MF +FPRL ER+ QLAGT+SGGEQQMLAM RALM P+VLLLDEPSMGL+P +V ++F Sbjct: 121 MFALFPRLAERRTQLAGTLSGGEQQMLAMARALMLNPRVLLLDEPSMGLAPRLVAEVFST 180 Query: 185 VRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 + + +T++LVEQ A+ AL +AD GYVME+G + GP L NDP VRAAYLG Sbjct: 181 IARLKEEKITMLLVEQFAAAALEVADFGYVMENGRLAAHGPAAMLKNDPAVRAAYLG 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: 167 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: 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