GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Cupriavidus basilensis 4G11

Align KguT (characterized, see rationale)
to candidate RR42_RS04270 RR42_RS04270 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Cup4G11:RR42_RS04270
          Length = 434

 Score =  212 bits (539), Expect = 2e-59
 Identities = 128/407 (31%), Positives = 210/407 (51%), Gaps = 22/407 (5%)

Query: 14  IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73
           ++P + + Y +AYLDR N GFA    M  DL  +  +  L   +FF+GYF F+VP  +  
Sbjct: 27  LVPFLLLCYVVAYLDRVNVGFAKLQ-MLGDLKFSETIYGLGAGIFFIGYFLFEVPSNVIL 85

Query: 74  EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133
            K   +  I   +I WG ++     V + ++   +RFLLG+ EA   P +++YL +W+  
Sbjct: 86  HKVGARIWIARIMITWGVISAAMMFVTTPTMFYVLRFLLGIAEAGFFPGIILYLTYWYPS 145

Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAFIWW 186
             R R  TF +    ++ +    +SG++++ FD       W+WMF++EG+P+VL   +  
Sbjct: 146 HRRGRTTTFFMTAIALSGVIGGPLSGWMMQSFDGRNGWSGWQWMFLLEGIPSVLVGLVVL 205

Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSIG 246
             +DDR   A WL  +EK  L+  +AAE    K      +   SP+V ++S  YF + +G
Sbjct: 206 AYLDDRIVHAKWLSNEEKALLQRNIAAEDMH-KEDAPIGKVLSSPRVWLMSAIYFSFVMG 264

Query: 247 VYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPLL 306
           +YG   WLP+I+KQ      +  G L+A+PY  AV  M+ V++++DR ++R+  +  P L
Sbjct: 265 LYGVSFWLPTIIKQTGVKSPLDIGLLTAIPYGCAVAGMVLVAYSADRTRERRWHIAIPAL 324

Query: 307 IAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-----PFFAIVP-ELLPSNVAGGA 360
           + A+      +L  +  W + T+L + G  + A  G     P F  +P   L    A   
Sbjct: 325 LGAVGL----VLSVQ--WHNNTVLALLGLTL-ATIGILTTLPLFWSLPTAFLAGTGAAAG 377

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALT 407
           +ALINS+G L  F   + VG+L  +T    +    +   L+   ALT
Sbjct: 378 IALINSLGNLAGFISPYAVGWLKDMTQSTDSGMYLLAACLVAGAALT 424


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: 625
Number of extensions: 38
Number of successful extensions: 5
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: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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