Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate GFF1917 PGA1_c19490 ABC transporter, inner-membrane protein
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Phaeo:GFF1917 Length = 294 Score = 144 bits (362), Expect = 3e-39 Identities = 88/274 (32%), Positives = 148/274 (54%), Gaps = 7/274 (2%) Query: 42 PFVLMSIAVYGG-TGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVL 100 PFV++ + ++ G G++ +SFT+ + L D+ LD Y + + +I + +N L+ Sbjct: 18 PFVVIVLLIFVGCVGWSVQLSFTNSKLLPNGDFVGLD--QYYRLFRTTRWIVSLKNMLLF 75 Query: 101 LVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILN 160 V F + L+LG LAILLD IR F+T++L P SLSFVVT W W N G+ N Sbjct: 76 GVFFVSGALILGFLLAILLDQKIRAEAFFRTIFLYPYSLSFVVTGLAWQWFLNPSLGLQN 135 Query: 161 LVVTTLGFN--PVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVD 218 V LG++ DWL + S+A+ +++A IW SG M + LAGL+ + + + A+++D Sbjct: 136 -AVRELGWSSFTFDWLTDQSMAIYTIVIAAIWHGSGLVMALMLAGLRGVDPEIWRASKID 194 Query: 219 GASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVR 278 G R Y+ I+ P L ++ V+L + +K F + A+ P T++ A ++ Sbjct: 195 GIPTWRVYVHIVAPILGPVIFASVVLLSLSVVKGFDIVVAMTNG-GPGIATEVPAKFVLD 253 Query: 279 RAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQY 312 + + A AT++LI + + P+LY Q+ Sbjct: 254 HILERANVGLAMAGATIMLITVISALAPWLYVQH 287 Lambda K H 0.326 0.140 0.424 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: 234 Number of extensions: 13 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: 317 Length of database: 294 Length adjustment: 27 Effective length of query: 290 Effective length of database: 267 Effective search space: 77430 Effective search space used: 77430 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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