Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate SMc04395 SMc04395 ABC transporter permease
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Smeli:SMc04395 Length = 292 Score = 159 bits (403), Expect = 6e-44 Identities = 94/277 (33%), Positives = 152/277 (54%), Gaps = 10/277 (3%) Query: 43 FVLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLV 102 F+++ + VYG Y +S TD + L P Y+ + L Y++ + + A N + Sbjct: 20 FLIVLVFVYGFIAYTGFLSMTDSKML--PSYNFVGLSNYSRLWALPHWWRAVSNLAIFAT 77 Query: 103 GFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLV 162 + +C VLGL LAILLD IR + VYL PM+LSF+VT W W + G+ N + Sbjct: 78 LYIAVCSVLGLALAILLDQKIRAEGFLRPVYLYPMALSFIVTGTAWKWFLDPGIGLENTM 137 Query: 163 VT----TLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVD 218 + FN W+ + + A+ V++A +WQ +G+ M ++LAGL+ + ++ +AA++D Sbjct: 138 HLWGWESFSFN---WIKDRNYAIYCVVIAAVWQSTGFIMAMFLAGLRGVDNEIIKAAQID 194 Query: 219 GASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVR 278 GA+ Y RII+P ++ +SA VVL A+KA+ + AL G P T++ AT M Sbjct: 195 GATTPTIYRRIIIPLMRPVFLSAFVVLAHLAIKAYDLIIALTGG-GPGQATELPATFMYS 253 Query: 279 RAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQYKQG 315 F + A A+ A ++L+M +I PYLY + + G Sbjct: 254 YTFTRNQMAIGASSAIVMLVMIFSIIVPYLYSEVRGG 290 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: 260 Number of extensions: 16 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: 292 Length adjustment: 27 Effective length of query: 290 Effective length of database: 265 Effective search space: 76850 Effective search space used: 76850 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