Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 371 bits (953), Expect = e-107 Identities = 205/504 (40%), Positives = 315/504 (62%), Gaps = 16/504 (3%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVY-PAGT 59 ++ L + +ITKTFPGVKAL +V+L + G++ AL+GENGAGKST++K+L+G+Y P G Sbjct: 16 VSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDG- 74 Query: 60 YEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEV-ASNGVISWQ 118 G I +G F + D G+ IHQE L LS+AENIFLG+ + G+I W+ Sbjct: 75 --GRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWK 132 Query: 119 QTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178 +T R LL +G + P+ + D+G+ + LV IA+ALS +++I+DEPTA+L+ + Sbjct: 133 KTTENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKE 192 Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238 E L L+ + QG + I+HK +E+ ++AD TV RDG + D +++E ++ Sbjct: 193 IEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIG--DGAIADVTEADLV 250 Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298 + MVGRD+ +P R +G+T+L V+ + H D DI+ T+R+GE++G GL Sbjct: 251 KMMVGRDVSQIFPQRAPNVGDTVLTVQGYA--HPTEFD-----DISFTLREGEILGFYGL 303 Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358 +GAGR+EF S+FG + G V I G ++S+ A+D G+ YV EDR G +L+ Sbjct: 304 VGAGRSEFMQSLFGIT--RPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILD 361 Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418 I N TL +L +S+ + +E +A ++ RL +R++ + NLSGGNQQKVV Sbjct: 362 LPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVV 421 Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478 ++KWL + P V+ILDEPT+G+D+G+K ++ + +LAA G V+M+SSE+PE+LG DR+ Sbjct: 422 IAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRV 481 Query: 479 YVMNEGRIVAELPKGEASQESIMR 502 VM EGRIVAEL + E+++R Sbjct: 482 IVMREGRIVAELAGDDLQPETLVR 505 Score = 65.5 bits (158), Expect = 4e-15 Identities = 59/257 (22%), Positives = 115/257 (44%), Gaps = 14/257 (5%) Query: 251 PPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSV 310 P D P+ + L + + + + L D+++++ G+V + G GAG++ + Sbjct: 10 PSEDPPVSQAALALAHIT---KTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKIL 66 Query: 311 FGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLND--NILHNTTLA 368 G G +L+DG+PV ST + A D G+ + H VL D ++ N L Sbjct: 67 TGIYQPDG--GRILVDGQPVPFSTPQAAADHGVTAI-----HQETVLFDELSVAENIFLG 119 Query: 369 NLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPD 428 + A +ID K + A T + + +L N+ V +++ L Sbjct: 120 H-APRGAFGLIDWKKTTENARALLTSIGAELDPD-HKLKDLGIANKHLVAIARALSIEAR 177 Query: 429 VLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVA 488 V+I+DEPT + E+Y ++ L A GK +L IS + E+ D V +G+++ Sbjct: 178 VVIMDEPTAALSHKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIG 237 Query: 489 ELPKGEASQESIMRAIM 505 + + ++ +++ ++ Sbjct: 238 DGAIADVTEADLVKMMV 254 Lambda K H 0.316 0.135 0.374 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: 599 Number of extensions: 28 Number of successful extensions: 11 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: 512 Length of database: 510 Length adjustment: 35 Effective length of query: 477 Effective length of database: 475 Effective search space: 226575 Effective search space used: 226575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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