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 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 129 bits (323), Expect = 1e-34 Identities = 85/249 (34%), Positives = 140/249 (56%), Gaps = 18/249 (7%) Query: 25 IKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVIT 84 + L++E + K + + + VSL +G++ +L+G SGSGKST+LR + E+P G I Sbjct: 19 VLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIY 78 Query: 85 LDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144 LDG I T P ++ N M+FQ + L+ HMTV +NI ++ +S Sbjct: 79 LDGQDI--------TDLPPYERPIN------MMFQSYALFPHMTVEQNIAFGLKQD-KMS 123 Query: 145 AAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALD 204 A+ +R + L V + + A + P LSGGQ+QRVA+AR+LA P+++L DEP ALD Sbjct: 124 KADISQRVQEMLKLVHM-EQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALD 182 Query: 205 PELVGEV-LKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDAR-ILDQP 262 +L ++ L+V++ L G T +MVTH+ A ++ ++ + G + + G I + P Sbjct: 183 KKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESP 242 Query: 263 NSERLQQFL 271 NS + +F+ Sbjct: 243 NSRMIAEFI 251 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: 222 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: 378 Length adjustment: 28 Effective length of query: 248 Effective length of database: 350 Effective search space: 86800 Effective search space used: 86800 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: 48 (23.1 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