Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__azobra:AZOBR_RS23525 Length = 269 Score = 249 bits (636), Expect = 4e-71 Identities = 134/249 (53%), Positives = 170/249 (68%), Gaps = 10/249 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKI--- 79 I+I + K +G VL+D++LTV V+ GPSGSGKST++RC N LE G+I Sbjct: 2 IEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRIN 61 Query: 80 ----IVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAE 135 I DG L K ++ +R+E GMVFQ FNLFPH+T +EN+ AP+ VR + K EA Sbjct: 62 HRTIIADGKPLPD--KELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEAR 119 Query: 136 ETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKE 195 E AM L KV + ++A YP LSGGQ+QR AIAR+L MKPK+MLFDEPTSALDPE++ E Sbjct: 120 ELAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVGE 179 Query: 196 VLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQ 255 VL M LAEEGMTM+ VTHEMGFA+ VA+ V+ MADG+IVE +P F NP ERT+ Sbjct: 180 VLQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTRG 239 Query: 256 FLSQIL-GH 263 FL ++ GH Sbjct: 240 FLRALVDGH 248 Lambda K H 0.320 0.134 0.391 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: 190 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: 263 Length of database: 269 Length adjustment: 25 Effective length of query: 238 Effective length of database: 244 Effective search space: 58072 Effective search space used: 58072 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 (21.8 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