Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate 206677 DVU1238 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >MicrobesOnline__882:206677 Length = 246 Score = 81.6 bits (200), Expect = 1e-20 Identities = 75/244 (30%), Positives = 118/244 (48%), Gaps = 9/244 (3%) Query: 9 AALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTW 68 AALLL +T A + + F +PP E V A+ + G ++ +AI + K Sbjct: 10 AALLL---STNVAFAERTVVFAHDATWPPMEFVDANKQIVGLAVDYVDAIAKEAGFKVVH 66 Query: 69 VHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPE 128 + +DG+ L A K+DAI SS+ +T R+K +DF+ F +++ K+ + T E Sbjct: 67 KNVAWDGIFAGLAAGKYDAIASSVTITEERKKAMDFTMPYFDVKQALVVPKTTE-AKTLE 125 Query: 129 SLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQL 188 + GK +G Q S +A A G K+Y DL NGR+D + D A Sbjct: 126 DMKGKTLGA-QISTTGHFAIKRTA--GVTAKSYDEIGLAMEDLFNGRIDGVVCDDPVA-A 181 Query: 189 NFLSKPEGSDFKTGPAFKDPTLPLD-IAMGLRKNDQALRALINKGIAAVQADGTYAQIQK 247 N+ + E K AF T + + +++ ++ L LINKGI AV+A G AQ++ Sbjct: 182 NYALQQEEYAKKLKIAFIVDTPESEYYGIAVKQGNKELVDLINKGIEAVKAKGIDAQLRA 241 Query: 248 KYFG 251 K+ G Sbjct: 242 KWIG 245 Lambda K H 0.319 0.135 0.393 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: 140 Number of extensions: 6 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: 258 Length of database: 246 Length adjustment: 24 Effective length of query: 234 Effective length of database: 222 Effective search space: 51948 Effective search space used: 51948 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