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 CCNA_02006 CCNA_02006 lipoprotein releasing system ATP-binding protein lolD
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Caulo:CCNA_02006 Length = 228 Score = 138 bits (348), Expect = 9e-38 Identities = 93/230 (40%), Positives = 130/230 (56%), Gaps = 16/230 (6%) Query: 27 LQVEGIHKRY----GEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGV 82 L + G+ + Y G+ VL+GV L+ G+V+ LIG SGSGKS++L LE+PDAG+ Sbjct: 6 LALRGLERVYKTEAGDLPVLRGVDLDVYPGEVVGLIGPSGSGKSSLLHSAGLLERPDAGL 65 Query: 83 ITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLD 142 + L+G RA TR L T + V+Q +L + LEN+ M P + Sbjct: 66 VALEGRDCSKLSERARTRI-------RLGT-VGFVYQFHHLLPEFSALENVAM-PLTIAG 116 Query: 143 VSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSA 202 S EAE RAR L+ +GL R+ Q PA +SGG+QQRVAIARALA P+++L DEPT Sbjct: 117 KSRREAEARARELLESLGLGHRLNHQ-PAQMSGGEQQRVAIARALANRPKLLLADEPTGN 175 Query: 203 LDPELVGEVLKVI-QTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVE 251 LDP V + + Q E+G ++ TH M AR + +V+ L G +E Sbjct: 176 LDPATSTAVFQALYQVCREQGVAAVIATHNMELARYM-DRVVALKDGHLE 224 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: 146 Number of extensions: 10 Number of successful extensions: 3 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: 228 Length adjustment: 24 Effective length of query: 252 Effective length of database: 204 Effective search space: 51408 Effective search space used: 51408 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: 46 (22.3 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