Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_004321579.1 C665_RS15455 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000310185.1:WP_004321579.1 Length = 237 Score = 238 bits (608), Expect = 6e-68 Identities = 122/233 (52%), Positives = 173/233 (74%), Gaps = 2/233 (0%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+++G+ YG I A++G+D EV+ GE+V+LIG+NGAGK+T M ++ G + G I + Sbjct: 1 MLKMEGVHAHYGHIHALRGIDVEVQVGEIVTLIGANGAGKSTLMMSLFGNPKASAGRIVF 60 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 G+ I ++ + G+ +VPEGR +F RMT+ ENLQMG D A AD ++F + Sbjct: 61 DGEDITRVHTHEIARRGIALVPEGRRIFPRMTVIENLQMGT-AHADPANYAADTARVFAM 119 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 FP L+ER+ Q AGT+SGGEQQMLA+GRALMS+PK+LLLDEPS+GL+PI + KIF++VR++ Sbjct: 120 FPILQERQAQRAGTLSGGEQQMLAIGRALMSRPKLLLLDEPSLGLAPIYIRKIFQIVREL 179 Query: 189 YA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 G+TI+LVEQNA++AL +ADRGYV++ G IT+ G G +LL P+VRAAYL Sbjct: 180 NRDHGMTILLVEQNANQALRVADRGYVLQHGEITLAGTGAELLASPEVRAAYL 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: 179 Number of extensions: 4 Number of successful extensions: 3 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: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 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