Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS00690 AZOBR_RS00690 ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__azobra:AZOBR_RS00690 Length = 268 Score = 305 bits (782), Expect = 5e-88 Identities = 159/249 (63%), Positives = 195/249 (78%), Gaps = 3/249 (1%) Query: 29 VEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLDGI 88 VE +HKR+G EVLKGVSL AR+GDVI+LIG+SGSGKST+LRCIN LE PD G I + G Sbjct: 17 VENVHKRFGPLEVLKGVSLTAREGDVITLIGSSGSGKSTLLRCINMLEVPDEGRIVIGGE 76 Query: 89 SIEMRQGRAGTRAPHQD-QLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAAE 147 +I +++ R G P Q+ +RTRL MVFQ FNLW+HMT+LEN+ AP VL V AE Sbjct: 77 AIGLKKARGGQTVPADSRQVDRIRTRLGMVFQSFNLWTHMTILENVIEAPVHVLGVPKAE 136 Query: 148 AEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPEL 207 A RAR LDKVG+ ++ A+ YP LSGGQQQR AIARALAM+P+++LFDEPTSALDPEL Sbjct: 137 AVDRARKLLDKVGILAK-AESYPVQLSGGQQQRAAIARALAMQPKVMLFDEPTSALDPEL 195 Query: 208 VGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDA-RILDQPNSER 266 VGEVL VI+ LAEEG TM++VTHEMGFAR+V+S+V+FLHQGR+EE G R+L P S+R Sbjct: 196 VGEVLLVIRQLAEEGNTMILVTHEMGFAREVASEVVFLHQGRIEERGPPDRVLVNPESDR 255 Query: 267 LQQFLSNRL 275 ++QFLS L Sbjct: 256 VRQFLSRHL 264 Lambda K H 0.319 0.133 0.372 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: 252 Number of extensions: 13 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: 276 Length of database: 268 Length adjustment: 25 Effective length of query: 251 Effective length of database: 243 Effective search space: 60993 Effective search space used: 60993 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