GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Cupriavidus basilensis 4G11

Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate RR42_RS34970 RR42_RS34970 bifunctional D-altronate/D-mannonate dehydratase

Query= BRENDA::G3Y8T6
         (383 letters)



>FitnessBrowser__Cup4G11:RR42_RS34970
          Length = 403

 Score =  172 bits (436), Expect = 1e-47
 Identities = 124/398 (31%), Positives = 186/398 (46%), Gaps = 47/398 (11%)

Query: 19  VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77
           +K+   E   G G+ATL G   AV   L D +   ++G +   +E +WQ ++R  ++R G
Sbjct: 20  LKIETDEGLSGIGDATLNGRELAVASYLEDHVAPCLIGRDPHQVEDIWQYLYRGAYWRRG 79

Query: 78  PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGGDRPSDVEVAAKARI 137
           PV MSA++ +D ALWD+K +   +P+YQLLGGK R  V VY    G   SD+E      +
Sbjct: 80  PVTMSAIAAVDTALWDIKAKAAGMPLYQLLGGKSRTGVMVYGHANG---SDIEATVDEVL 136

Query: 138 AQ---GLKCVKMNA-----------TEDMNWLDS-----PSVLDSCIERI---------K 169
                G + V+  +           + D  + +      PS  D   ER          K
Sbjct: 137 RYKELGYRAVRAQSGVPGLNKVYGVSSDRLFYEPADASLPSEHDWSTERYLDHTPRLFEK 196

Query: 170 QVKALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTI 227
              A G D  L  D H RL    A +L K+LEP+R  ++E+    EH E+ + + QHTT 
Sbjct: 197 VRDAAGWDLHLLHDVHHRLTPIEAARLGKSLEPFRLFWMEDATPAEHQESFRLIRQHTTT 256

Query: 228 PIAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPH--CP 285
           P+A GE   T WD K  +++  +D ++  + HAGGI+  +RIA  A  + V    H    
Sbjct: 257 PLAVGEVFNTIWDCKTLIQEQLIDYIRATVVHAGGITHLRRIADFAAMHQVRTGSHGATD 316

Query: 286 LGPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPT 345
           L P+ + A++   L  PNF IQE    M ++ +   +        P  +    G +    
Sbjct: 317 LSPVCMGAALHFDLWVPNFGIQEY---MRHSEQTDAV-------FPHAYTFANGMLYPGD 366

Query: 346 GAGLGVEIDEELVRRISRETEPWLPKEFYGVDGGIREW 383
             G GV+IDE L  R   +   +LP      DG +  W
Sbjct: 367 APGHGVDIDETLAARYPYQ-RAYLPVNRLAHDGTLWHW 403


Lambda     K      H
   0.320    0.138    0.425 

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: 412
Number of extensions: 28
Number of successful extensions: 4
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: 383
Length of database: 403
Length adjustment: 31
Effective length of query: 352
Effective length of database: 372
Effective search space:   130944
Effective search space used:   130944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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