Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate 5210738 Shew_3166 extracellular solute-binding protein (RefSeq)
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__PV4:5210738 Length = 242 Score = 83.2 bits (204), Expect = 5e-21 Identities = 71/247 (28%), Positives = 111/247 (44%), Gaps = 21/247 (8%) Query: 8 FAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVA--ADGSLQGFDIELGNAICAKLEVK 65 F ALLL L Q++ + G +PPFE V + + GFDI+L + Sbjct: 10 FTALLL-LSGCGKEQDYLVV--GTNAAFPPFEYVGGVSGDQVMGFDIDLARKVAEDAGKT 66 Query: 66 CTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGD 125 + +FD +I AL A K D I S M +TP R+ +DFS+ + + V+ K D Sbjct: 67 LKVENMKFDSLIVALNAGKIDMIASGMTITPERQASVDFSEPYYEATQVVLVNKQDDSIH 126 Query: 126 TPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLE 185 + L GK V GS + A+ K + A+ + + +L+NG++D L D E Sbjct: 127 SLADLTGKHFAVQLGSTADMMAK----KYTQSVTAFNTGFEAIMELKNGKVDLVLFDS-E 181 Query: 186 AQLNFLSKPEGSDFKTGPAFKDPTL---PLDIAMGLRKNDQALRALINKGIAAVQADGTY 242 N+L+K P K +L P + K+ L A INK +A ++ +G Y Sbjct: 182 PAANYLAK--------NPELKLISLDFPPEFYGFAVAKSQPELLASINKTLATMKQNGEY 233 Query: 243 AQIQKKY 249 + K+ Sbjct: 234 DALLAKH 240 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: 142 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: 258 Length of database: 242 Length adjustment: 24 Effective length of query: 234 Effective length of database: 218 Effective search space: 51012 Effective search space used: 51012 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