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 GFF1457 HP15_1422 amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Marino:GFF1457 Length = 240 Score = 229 bits (585), Expect = 3e-65 Identities = 124/247 (50%), Positives = 169/247 (68%), Gaps = 12/247 (4%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 + V+ +HK +G+ EVLKGVSL+ ++G+V+S+IG SGSGKST+L CIN +E + G I +D Sbjct: 2 ISVQNVHKSFGDLEVLKGVSLDVKKGEVVSVIGGSGSGKSTLLYCINAIEPINKGKILVD 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 + + ++ LR +L MVFQ +N + HMTVLEN +APR V +S Sbjct: 62 DVDVHAKETNK----------DKLRQKLGMVFQQWNSFPHMTVLENAALAPRIVKKMSKE 111 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 EA + A+ L+ VGL + D YP +SGGQQQR+AIARALAM+P+ +L DE TSALDPE Sbjct: 112 EAIEIAKKELEHVGLGDKF-DVYPTKMSGGQQQRLAIARALAMKPDYMLLDEVTSALDPE 170 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDAR-ILDQPNSE 265 LVGEVL ++ LAEEG TM+ VTHEMGFAR VS +V + H+G + E G+AR ++ P + Sbjct: 171 LVGEVLDTLRLLAEEGMTMICVTHEMGFARDVSDRVAYFHEGVIAEIGEARQVITDPQNP 230 Query: 266 RLQQFLS 272 Q+FLS Sbjct: 231 LTQKFLS 237 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: 194 Number of extensions: 8 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: 240 Length adjustment: 24 Effective length of query: 252 Effective length of database: 216 Effective search space: 54432 Effective search space used: 54432 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