Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate WP_007695789.1 C447_RS16065 carbohydrate ABC transporter permease
Query= uniprot:D4GP37 (309 letters) >NCBI__GCF_000336675.1:WP_007695789.1 Length = 305 Score = 355 bits (910), Expect = e-102 Identities = 168/288 (58%), Positives = 223/288 (77%), Gaps = 2/288 (0%) Query: 20 NLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVGEGFTLGNIQFALE 79 +L R Y L++FF+ FFLVPLETG+MTA KT + V +LPF PP+GE FT A + Sbjct: 18 DLSRALLYLLILFFVAFFLVPLETGLMTAFKTTQGVTNTLPFFPPLGEAFTFQKWVDAFD 77 Query: 80 QLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFVPYQAVLVP 139 L NS+++++PAT+ +LFGS AAYGLT++NWR Q+ +L+LF++G+F+PYQAVLVP Sbjct: 78 MLGRGLVNSMVLTVPATLLCLLFGSTAAYGLTLINWRGQIFVLVLFLIGIFIPYQAVLVP 137 Query: 140 LARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSLPN 199 L+RFW+ + PL + P+ + F Q HA+LV L+IT AYGIPICT+LFR YY SLP Sbjct: 138 LSRFWSMV-PLEEWLSPLYV-LSFVQPEHAQLVELIITDAAYGIPICTLLFRGYYLSLPG 195 Query: 200 SLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPAAP 259 L+EA K+DGAS+T IYRRI+LP+S PM GVVFIYQFTQI+NEFLF T+V +D+PAAP Sbjct: 196 DLIEAAKLDGASVTSIYRRIVLPLSTPMIGVVFIYQFTQIWNEFLFTLTIVGSADSPAAP 255 Query: 260 VTLVLPAIGASTSGINFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRT 307 VTL+L +G+S SG++FG+RM+ AF+AA+PTL++YV FAEQFA+GL T Sbjct: 256 VTLILSGLGSSLSGVDFGMRMAGAFIAALPTLVIYVLFAEQFAEGLET 303 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: 344 Number of extensions: 14 Number of successful extensions: 2 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: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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