Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate WP_007695788.1 C447_RS16060 sugar ABC transporter permease
Query= uniprot:D4GP36 (317 letters) >NCBI__GCF_000336675.1:WP_007695788.1 Length = 324 Score = 412 bits (1058), Expect = e-120 Identities = 197/296 (66%), Positives = 238/296 (80%) Query: 22 SKLRYFLNSDFVRSAPYWGIPFVLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMY 81 S+LR SDFVRS PYW +PFV+M VYGG G+N +S TDY G G+ DY LD EMY Sbjct: 29 SRLRSISESDFVRSMPYWFVPFVIMGFFVYGGIGWNLLVSLTDYTGFGSADYGDLDFEMY 88 Query: 82 AQALSSDAFIAAAQNNLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSF 141 QALSS IAA++N VLLV FT +CLVLGL LAI+LD IRF E+ QT+YLLPM+LSF Sbjct: 89 VQALSSPDVIAASRNTFVLLVVFTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSF 148 Query: 142 VVTAQLWLWMFNVESGILNLVVTTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYL 201 VVTAQ WLWM+N SG++N+++ +G + ++G+P LGAVI ALIWQFSGYTM+VYL Sbjct: 149 VVTAQFWLWMYNYNSGVINIILDAVGIGRIQFIGDPRFVLGAVIFALIWQFSGYTMIVYL 208 Query: 202 AGLQSIPDDQFEAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVG 261 +GLQSIP DQFEAA DGAS + Y R+I+PQLK ASVSAAVVLM+FALKAFTFLY++ G Sbjct: 209 SGLQSIPQDQFEAAATDGASTVKIYWRVIIPQLKSASVSAAVVLMIFALKAFTFLYSMFG 268 Query: 262 RYRPPNGTDILATLMVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQYKQGGL 317 YRPPNG+DILATLMVR+AFKF EW+Y+AA+AT+LL+MAL VIGPYLYYQY++G L Sbjct: 269 TYRPPNGSDILATLMVRQAFKFQEWSYAAAVATLLLLMALVVIGPYLYYQYQRGSL 324 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: 374 Number of extensions: 11 Number of successful extensions: 1 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: 324 Length adjustment: 28 Effective length of query: 289 Effective length of database: 296 Effective search space: 85544 Effective search space used: 85544 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 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