Align ABC transporter related (characterized, see rationale)
to candidate AZOBR_RS00690 AZOBR_RS00690 ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__azobra:AZOBR_RS00690 Length = 268 Score = 326 bits (835), Expect = 4e-94 Identities = 159/256 (62%), Positives = 200/256 (78%) Query: 2 NATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPD 61 N AP A+ V+N+HK FG VLKG+SL A +GDVI+++G+SGSGKST LRC+N+LE PD Sbjct: 8 NPNAPEAVLVENVHKRFGPLEVLKGVSLTAREGDVITLIGSSGSGKSTLLRCINMLEVPD 67 Query: 62 DGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPM 121 +G + + GE + +K+ G+ P+D RQVDR+R++LGMVFQ+FNLW+HMT+LEN+IE P+ Sbjct: 68 EGRIVIGGEAIGLKKARGGQTVPADSRQVDRIRTRLGMVFQSFNLWTHMTILENVIEAPV 127 Query: 122 RVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEP 181 V +AE+V+ A LL KVG+ K YP LSGGQQQR AIARALAM PKVMLFDEP Sbjct: 128 HVLGVPKAEAVDRARKLLDKVGILAKAESYPVQLSGGQQQRAAIARALAMQPKVMLFDEP 187 Query: 182 TSALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEV 241 TSALDPELVGEVL V+R LAEEG TM++VTHEMGFAR V++ V+FLHQG++E G PD V Sbjct: 188 TSALDPELVGEVLLVIRQLAEEGNTMILVTHEMGFAREVASEVVFLHQGRIEERGPPDRV 247 Query: 242 FVECKSDRFRQFVSSH 257 V +SDR RQF+S H Sbjct: 248 LVNPESDRVRQFLSRH 263 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: 243 Number of extensions: 6 Number of successful extensions: 1 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: 268 Length adjustment: 25 Effective length of query: 238 Effective length of database: 243 Effective search space: 57834 Effective search space used: 57834 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: 47 (22.7 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