Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 126 bits (316), Expect = 7e-34 Identities = 81/273 (29%), Positives = 143/273 (52%), Gaps = 7/273 (2%) Query: 34 RSAPYWGIP--FVLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFI 91 R +PY + ++ + V+ F SFT ++ T + LE + + L+ F Sbjct: 7 RLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFW 66 Query: 92 AAAQNNLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWM 151 N + L+G + + L L LAIL++ +R F+ Y P+ +S VV W W+ Sbjct: 67 KTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAWRWL 126 Query: 152 FNVESGILNLV---VTTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIP 208 + E+G+LN + V GF P+ WL +P++AL +V+ +W+ GY MV+YLAGLQ IP Sbjct: 127 Y-AETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGIP 185 Query: 209 DDQFEAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNG 268 + +EAA +DG+ R +L I +P ++ V AV+ + A K F ++ ++ + P N Sbjct: 186 LELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVF-IMTQGGPLNS 244 Query: 269 TDILATLMVRRAFKFGEWAYSAAIATMLLIMAL 301 + + + ++AF+ E +Y+ + L ++ L Sbjct: 245 SKTVVYYVYQQAFQKLEVSYACTVGLALFLVVL 277 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: 252 Number of extensions: 11 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: 317 Length of database: 293 Length adjustment: 27 Effective length of query: 290 Effective length of database: 266 Effective search space: 77140 Effective search space used: 77140 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