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 16031 b1917 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Keio:16031 Length = 250 Score = 229 bits (583), Expect = 6e-65 Identities = 128/250 (51%), Positives = 167/250 (66%), Gaps = 6/250 (2%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 ++V+ + K++ VL G+ L + G+V+++IG SGSGK+T+LR IN LEQP+AG IT+ Sbjct: 4 IEVKNLVKKFHGQTVLHGIDLEVKPGEVVAIIGPSGSGKTTLLRSINLLEQPEAGTITVG 63 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 I+I+ A + + + ++ LR + VFQ+FNL+ H TVLENI P V Sbjct: 64 DITIDT----ARSLSQQKSLIRQLRQHVGFVFQNFNLFPHRTVLENIIEGPVIVKGEPKE 119 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 EA RAR L KVGL + YP LSGGQQQRVAIARALAM PE+ILFDEPTSALDPE Sbjct: 120 EATARARELLAKVGLAGKETS-YPRRLSGGQQQRVAIARALAMRPEVILFDEPTSALDPE 178 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDARIL-DQPNSE 265 LVGEVL I+ LA+E RTM++VTHEM FAR V+ + +F+ QGR+ E G A+ L P Sbjct: 179 LVGEVLNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFMDQGRIVEQGAAKALFADPEQP 238 Query: 266 RLQQFLSNRL 275 R +QFL L Sbjct: 239 RTRQFLEKFL 248 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: 219 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: 250 Length adjustment: 25 Effective length of query: 251 Effective length of database: 225 Effective search space: 56475 Effective search space used: 56475 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