Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate AZOBR_RS00690 AZOBR_RS00690 ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__azobra:AZOBR_RS00690 Length = 268 Score = 236 bits (602), Expect = 4e-67 Identities = 127/257 (49%), Positives = 174/257 (67%), Gaps = 12/257 (4%) Query: 8 PVSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQ 67 P +PE ++ ++ V+K +G VLK ++L ++G+ I L G SGSGKST +RC+N LE Sbjct: 9 PNAPEAVL-VENVHKRFGPLEVLKGVSLTAREGDVITLIGSSGSGKSTLLRCINMLEVPD 67 Query: 68 QGRIVVDGVEL-----------TNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPM 116 +GRIV+ G + D +Q++ IR +GMVFQ FNL+ H+TIL+N AP+ Sbjct: 68 EGRIVIGGEAIGLKKARGGQTVPADSRQVDRIRTRLGMVFQSFNLWTHMTILENVIEAPV 127 Query: 117 WVRKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEP 176 V +PK +A + A L++V I +A YP QLSGGQQQR AIARAL M+PK+MLFDEP Sbjct: 128 HVLGVPKAEAVDRARKLLDKVGILAKAESYPVQLSGGQQQRAAIARALAMQPKVMLFDEP 187 Query: 177 TSALDPEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDF 236 TSALDPE+V EVL + LAE+G TM+ VTHEMGFAR VA+ V+F+ +G I E+ P+ Sbjct: 188 TSALDPELVGEVLLVIRQLAEEGNTMILVTHEMGFAREVASEVVFLHQGRIEERGPPDRV 247 Query: 237 FDNPQNDRTKLFLSQIL 253 NP++DR + FLS+ L Sbjct: 248 LVNPESDRVRQFLSRHL 264 Lambda K H 0.322 0.137 0.407 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: 215 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: 254 Length of database: 268 Length adjustment: 25 Effective length of query: 229 Effective length of database: 243 Effective search space: 55647 Effective search space used: 55647 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 (21.9 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