Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate RR42_RS34990 RR42_RS34990 ABC transporter permease
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS34990 Length = 467 Score = 266 bits (680), Expect = 1e-75 Identities = 164/449 (36%), Positives = 246/449 (54%), Gaps = 45/449 (10%) Query: 5 VFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVPFFIL 64 + + S L M +G+P+A A+ + + +W +LAQ + AG +SFPLLAVPFFIL Sbjct: 3 ILIVSFLLLMLVGLPVAIAMAVASLLYIWASGTVPDVILAQRMIAGVESFPLLAVPFFIL 62 Query: 65 AGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALATLLLP 124 AG LMN GI+ RI A A G RGGLG+V I SV+ + MSG+A+AD A L T+ + Sbjct: 63 AGNLMNVAGITGRIYNFAVALVGWMRGGLGHVNIIGSVIFSGMSGTAIADAAGLGTIEIK 122 Query: 125 MMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLIM--- 181 M++ GY + G+ AA + PIIPPS+PFVIYG++ SI LFLAG+VPGL++ Sbjct: 123 AMQDHGYETEFAVGVTAASATLGPIIPPSLPFVIYGMMANVSIGSLFLAGIVPGLVLTLF 182 Query: 182 --------------GMGLIVAWTLIARRIDEPKQEKAS-----AAERRRVLVDGAAALML 222 G +W L+ E A R V + AA + L Sbjct: 183 MMGTVAWFAHRRGWGSDTAFSWKLLGNASIEIAVVLAFPLAIWLMTRFGVSTNVAALIAL 242 Query: 223 --------------------PVIIVGGLRGGLFTPTEAAVVAAVYALAVSTLLYRELNWA 262 PVI++GG+ G FTPTEAAV A ++AL + + YR + Sbjct: 243 VVLLALDWYFDFSAVMALMAPVILIGGMTLGWFTPTEAAVAAVIWALFLGLVRYRSMTLR 302 Query: 263 GLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPDEIA-AMLGPLAQDPKLLMVAIML 321 L + TTASV+F+ AA++ A+++T +Q ++ A+LG L++A +L Sbjct: 303 SLAKATLDTIETTASVLFIVTAASIFAWLLTTSQAAQMLSDAILGFTHNKWVFLLLANVL 362 Query: 322 LMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVMFVLIGSIGLITPPVGTVLNVV 381 ++I VG +D T I IL P+L PI +K GIDP++FG++ L IGL+ PP+G VL V+ Sbjct: 363 ILI-VGCFIDTTAAITILVPILLPIVLKLGIDPIHFGLVMTLNLMIGLLHPPLGMVLFVL 421 Query: 382 GGIGRLRMETLVRGVMPFFL-IYLVIVGL 409 + +L +E ++P+ + ++L ++ + Sbjct: 422 ARVAKLSVERTTVAILPWLVPLFLTLIAI 450 Lambda K H 0.328 0.142 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: 642 Number of extensions: 33 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 425 Length of database: 467 Length adjustment: 32 Effective length of query: 393 Effective length of database: 435 Effective search space: 170955 Effective search space used: 170955 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: 51 (24.3 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