Align ABC transporter related (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 149 bits (375), Expect = 1e-40 Identities = 91/245 (37%), Positives = 139/245 (56%), Gaps = 19/245 (7%) Query: 7 VALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVS 66 +++ + NI K FG L ++LD +G++I +LG SGSGK+T LR + LE D G + Sbjct: 1 MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60 Query: 67 LAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENL---IEGPMRV 123 ++ ++ DRR +G VFQN+ L+ HMTV +N+ +E + Sbjct: 61 FGNRDVT-------QVHVRDRR--------VGFVFQNYALFRHMTVADNVAFGLEVIPKK 105 Query: 124 QKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTS 183 Q+ S+AE + LL V L YP LSGGQ+QR+A+ARALA P+V+L DEP Sbjct: 106 QRPSKAEIQKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFG 165 Query: 184 ALDPELVGEVLRVMRSLAEEGR-TMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242 ALD ++ E+ R +RSL +E + T + VTH+ A +S+RV+ + G +E TP E++ Sbjct: 166 ALDAKVRKELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELY 225 Query: 243 VECKS 247 + S Sbjct: 226 AQPNS 230 Lambda K H 0.318 0.133 0.377 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: 223 Number of extensions: 15 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: 263 Length of database: 376 Length adjustment: 27 Effective length of query: 236 Effective length of database: 349 Effective search space: 82364 Effective search space used: 82364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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