Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate WP_106712916.1 CU102_RS20280 carbohydrate ABC transporter permease
Query= uniprot:D4GP37 (309 letters) >NCBI__GCF_003010955.1:WP_106712916.1 Length = 316 Score = 130 bits (327), Expect = 4e-35 Identities = 88/293 (30%), Positives = 144/293 (49%), Gaps = 33/293 (11%) Query: 27 YALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVGEGF----TLGNIQFA---LE 79 Y+++ ++L+PL +MT++K + F+PPV F T N E Sbjct: 44 YSVLFVAAIYYLIPLYVMVMTSLKGMPEIRIGNIFSPPVEVTFQPWATAWNSACTGLYCE 103 Query: 80 QLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLML--FVVGVFVPYQAVL 137 + FFNS+ + +P+ I S++ S+ Y L+ NWR + L + G F+PYQ +L Sbjct: 104 GIKVGFFNSMKILVPSVILSIIIASVNGYALS--NWRFKGSELFFTALIFGAFIPYQVML 161 Query: 138 VPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSL 197 PL + G L +++ H +G+PI T+LFR+Y+ SL Sbjct: 162 YPLVIITRQL------------------GIFGTLTGVIVIHTIFGMPILTLLFRNYFVSL 203 Query: 198 PNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPA 257 P L +A ++DGA +I+ +I+LP+S P+F V I Q T I+N+FLF V + Sbjct: 204 PPELFKAARVDGAGFWRIFLQIMLPMSLPIFVVAVILQVTGIWNDFLFG---VIFAGTKN 260 Query: 258 APVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309 P+T+ L I ST G+ + + M+A L L++Y + F +G+ A Sbjct: 261 FPMTVQLNNIVNSTQGVKEYNVNMAATILTGAVPLLVYFFSGKYFVRGIAAGA 313 Lambda K H 0.328 0.141 0.413 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: 260 Number of extensions: 17 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: 309 Length of database: 316 Length adjustment: 27 Effective length of query: 282 Effective length of database: 289 Effective search space: 81498 Effective search space used: 81498 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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