GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Klebsiella michiganensis M5al

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate BWI76_RS19555 BWI76_RS19555 PTS beta-glucoside transporter subunit EIIBCA

Query= TCDB::P08722
         (625 letters)



>FitnessBrowser__Koxy:BWI76_RS19555
          Length = 619

 Score =  710 bits (1833), Expect = 0.0
 Identities = 348/622 (55%), Positives = 457/622 (73%), Gaps = 8/622 (1%)

Query: 4   LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63
           LA+ I+  VGG +NIVSL+HCATRLRFKLKD  KA AE LK  PG+IMVVESGGQFQVVI
Sbjct: 6   LAQDILTRVGGRENIVSLVHCATRLRFKLKDSKKADAEGLKANPGVIMVVESGGQFQVVI 65

Query: 64  GNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILKG 123
           GNHV DV+LAV S AGL + ++      +K +L+ + + ++SGIFTP IG++AA+GILKG
Sbjct: 66  GNHVHDVWLAVRSEAGLTDDSEPVAVKGEKVSLIGQLIDIVSGIFTPFIGVLAASGILKG 125

Query: 124 MLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALVH 183
           +LALA+   W T Q  TY I F+ASDALF+FFP+ LGYTAGK+FGGNPF  MVIGGAL H
Sbjct: 126 LLALAVVCGWLTTQQATYKIWFAASDALFFFFPLFLGYTAGKKFGGNPFITMVIGGALTH 185

Query: 184 PLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAIK 243
           PL++ AF+      A    FLGIPVT +NYSSSVIPII ++W+   +E+R NA LPS++K
Sbjct: 186 PLMIQAFDASMAPGAATEYFLGIPVTFINYSSSVIPIILASWVSCWIEKRSNAILPSSMK 245

Query: 244 NFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVMF 303
           NFFTP +CL V+ P+TFL++GP++TW+S+L+A GY  +YQ  P  AGA MG  WQ+ V+F
Sbjct: 246 NFFTPAICLAVVVPLTFLIIGPVATWLSQLLANGYQLIYQVAPWLAGAAMGALWQVCVIF 305

Query: 304 GLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALTS 363
           GLHWGL+PL INN  VLG+D+M+P+L+PA+M QVGAALG+FL  RDA++KV+AGSA    
Sbjct: 306 GLHWGLIPLMINNLAVLGHDSMMPMLLPAVMGQVGAALGIFLRTRDARQKVLAGSAVSAG 365

Query: 364 LFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPSTG 423
           +FG+TEPA+YG+NLP + PF+  C++GA+G  ++G++ + VYSFG  +IFT  Q IP  G
Sbjct: 366 IFGVTEPAIYGLNLPLRRPFIFGCVAGAIGGAMVGFSDSHVYSFGFGNIFTLAQMIPPEG 425

Query: 424 IDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPEQGGICSPM 483
           ID TVW    G   ++  A V T++         P   A  E+   V+ P  +  I +PM
Sbjct: 426 IDATVWGGAAGMFASLIIACVLTLVAGL------PRSSA--EQAAVVVAPASENDILAPM 477

Query: 484 TGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVE 543
           TG ++ L  V D+TFASGLLG+G+AI+PSVG+V +P +G +AS+F T HAIG+ SD G+E
Sbjct: 478 TGSVLALDQVPDSTFASGLLGQGVAIIPSVGKVIAPFSGEVASIFQTKHAIGLLSDSGIE 537

Query: 544 ILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDF 603
           +LIHVGIDTVKLDG  F+AHV  GDK+  GD L+ FD  AI +AG+DL TP++ISNSDDF
Sbjct: 538 LLIHVGIDTVKLDGAPFTAHVKEGDKIKAGDLLLEFDRQAILDAGYDLATPIIISNSDDF 597

Query: 604 TDVLPHGTAQISAGEPLLSIIR 625
             +     + + AG+PLLS+ R
Sbjct: 598 RTLDMVSASAVDAGQPLLSVSR 619


Lambda     K      H
   0.324    0.141    0.427 

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: 1322
Number of extensions: 76
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: 625
Length of database: 619
Length adjustment: 37
Effective length of query: 588
Effective length of database: 582
Effective search space:   342216
Effective search space used:   342216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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