Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_002117405.1:WP_085770499.1 Length = 266 Score = 179 bits (454), Expect = 5e-50 Identities = 96/245 (39%), Positives = 163/245 (66%), Gaps = 8/245 (3%) Query: 5 SNKVLLQVKGLKVAYG-GIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLS--- 60 + + LL+++ ++ +Y I A++ V +VR GE+V+L+G+NG+GKTT + A + L+ Sbjct: 3 ATETLLELRDVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAER 62 Query: 61 --MNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK-DKAG 117 + G I + G+S +L ++GLV V EGR VF +T+ ENL GA R+ ++ Sbjct: 63 GQITSGKILFDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRRE 122 Query: 118 ILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIM 177 + D++ ++ +FP+L+ R+ LAG +SGGEQQM A+GRA+M+ P++L+LDEPSMGL+P++ Sbjct: 123 LRDDLDYVYGVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLV 182 Query: 178 VDKIFEVVRDVYAL-GVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVR 236 V++I++V+ + + G+++++ EQNA AL A RGYV+E+G++ + G L V+ Sbjct: 183 VEEIYQVLGALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVK 242 Query: 237 AAYLG 241 YLG Sbjct: 243 DFYLG 247 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: 154 Number of extensions: 9 Number of successful extensions: 4 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: 266 Length adjustment: 24 Effective length of query: 218 Effective length of database: 242 Effective search space: 52756 Effective search space used: 52756 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: 47 (22.7 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