GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Paraburkholderia bryophila 376MFSha3.1

Align KguT (characterized, see rationale)
to candidate H281DRAFT_00211 H281DRAFT_00211 D-galactonate transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Burk376:H281DRAFT_00211
          Length = 439

 Score =  228 bits (580), Expect = 4e-64
 Identities = 140/420 (33%), Positives = 223/420 (53%), Gaps = 23/420 (5%)

Query: 12  WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71
           W + P++ + Y +AYLDR N GFA    M  DL ++ A+      +FF+GYFFF++P  +
Sbjct: 30  WRLAPLLMLCYVVAYLDRVNVGFAKLQ-MTSDLGLSDAVYGFGAGIFFVGYFFFEIPSNV 88

Query: 72  YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131
              K   +  I   ++ WG ++ LT  V + ++   +RFLLGV EA   P +++YL +W+
Sbjct: 89  ILHKVGARVWIARIMVSWGVISMLTMFVTTPTMFYVMRFLLGVAEAGFFPGIILYLTYWY 148

Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAFI 184
               R R  T+ +    ++ +    VSGY++K F+       W+W+F++EG+P+VL   +
Sbjct: 149 PSHRRGRMTTWFMTAIALSGVIGGPVSGYILKTFNGMNGWHGWQWLFLLEGIPSVLVGIL 208

Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244
            +  +DDR  +A WL  +EK  L   ++AE +  K     R+   S +V++LS  YF + 
Sbjct: 209 VFVALDDRISKAKWLTKEEKELLERHVSAE-EATKHDMPIRQVLTSGRVLMLSFTYFSFV 267

Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304
           +G+YG   WLP+I+K     D    G LSAVP+  AV+AM+ V+ ++DR ++R+   W  
Sbjct: 268 MGLYGVSFWLPTIIKATGVTDAFAIGLLSAVPFAAAVVAMVFVARSADRTRERR---WH- 323

Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-----PFFAIVP-ELLPSNVAG 358
             IA  AF G+  L     W   TLL +A   + A  G     P F  +P  +L    A 
Sbjct: 324 --IALPAFAGAIGLVLSVVWAQNTLLAMASLTL-ATMGILTTLPLFWSLPTAILAGTGAA 380

Query: 359 GAMALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARR 418
             +A+INS+G L  F   + VG+L   T     S ++M  A +V   L A+  P++   R
Sbjct: 381 AGIAMINSIGNLAGFLSPYAVGWLKQATAA-NDSGMYMLAAFMVVGGLLAISVPAKMVNR 439


Lambda     K      H
   0.328    0.140    0.457 

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: 610
Number of extensions: 35
Number of successful extensions: 8
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: 425
Length of database: 439
Length adjustment: 32
Effective length of query: 393
Effective length of database: 407
Effective search space:   159951
Effective search space used:   159951
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 (21.8 bits)
S2: 51 (24.3 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