Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000021745.1:WP_012589117.1 Length = 265 Score = 115 bits (289), Expect = 7e-31 Identities = 76/248 (30%), Positives = 121/248 (48%), Gaps = 15/248 (6%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 LL +KGL + YGG+ AV+ +D V EG L +LIG NGAGKT+ I+G +DG I Sbjct: 6 LLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDDGEIWL 65 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR---------------K 113 G I + GL + +F T EN+ +G ++ + Sbjct: 66 GGARIDRLSPSQRARRGLARTFQNLRLFTETTAIENVLVGMHLHVGGSLLEILTRFGRFR 125 Query: 114 DKAGILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGL 173 D + F L + AG++S G+Q+ L + RAL ++PK+LLLDEP+ G+ Sbjct: 126 QAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARALAAKPKLLLLDEPAAGM 185 Query: 174 SPIMVDKIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDP 233 +P + ++ + A ++++LVE + S + + D+ V+ G GP + +P Sbjct: 186 NPAETAALRLLLEKLRAQKISMLLVEHDMSLVMRLCDKITVLNFGRKIAEGPPDAVRANP 245 Query: 234 KVRAAYLG 241 V AYLG Sbjct: 246 AVIEAYLG 253 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: 132 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: 265 Length adjustment: 24 Effective length of query: 218 Effective length of database: 241 Effective search space: 52538 Effective search space used: 52538 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 Apr 09 2024. 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