GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Corynebacterium deserti GIMN1.010

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_082353398.1 CDES_RS06155 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= reanno::Smeli:SM_b20891
         (477 letters)



>NCBI__GCF_001277995.1:WP_082353398.1
          Length = 513

 Score =  275 bits (702), Expect = 3e-78
 Identities = 159/451 (35%), Positives = 235/451 (52%), Gaps = 3/451 (0%)

Query: 22  NPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILARKDEL 81
           NP+ T  V      A+     AA++AA+A  PAW  +G+  R A++ K  + I +RKDEL
Sbjct: 44  NPA-TGAVTASLPFATTATVNAAVSAAQAVAPAWRATGLARRAAVMFKLHEIITSRKDEL 102

Query: 82  GRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEITREPAGVV 141
             L++ E+GK L++  GE  R  +  EF AG    + GE +     G+ V   R+P GVV
Sbjct: 103 AALITEEQGKVLSDAAGEIARGLENVEFCAGLVHHMKGEFLEQAAAGLDVHQVRQPLGVV 162

Query: 142 GIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKGVLNLVM 201
             ITP+NFP  +P W +  A+  GNT+V KP+E  P     IV+  H AGLP+GVLNL+ 
Sbjct: 163 ACITPFNFPAMVPLWMITTAIAAGNTVVLKPSEKDPSAVNWIVEAFHEAGLPEGVLNLIH 222

Query: 202 GKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVVLDDADL 261
           G    V +A++D P VQA++F GST   + +   +    ++ Q   G KN  VV+ DADL
Sbjct: 223 GDREAV-EALIDDPRVQAVSFVGSTPIAQSIYTRATALGKRVQALGGAKNHMVVMPDADL 281

Query: 262 SVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKPGTHIGP 321
             A +AAV++ + + G+RC A S ++    I D  +A +  RI  L + +   P + +GP
Sbjct: 282 DAAADAAVSAGYGAAGERCMAISVVVPVGDIADDLIAKISSRITDLTIGEGTDPDSEMGP 341

Query: 322 VVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEATNEMRISREEIF 381
           V+  +   +    IA     GA++   G  +     GF++ P L       M +  EEIF
Sbjct: 342 VITSAAKERIEGLIAGSSDSGAEVVVDGRSVDLPDEGFFIGPTLIDHVKPGMPVYDEEIF 401

Query: 382 GPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVNLPTAGVD 441
           GPV +V RV  +DEA+ + N   +   + I T   + A  F+   E GMV +N+P     
Sbjct: 402 GPVLSVARVGHFDEAVELINSCQYANGTAIFTRDGRTAREFEFAIEVGMVGINVPIPVPI 461

Query: 442 FHVPFGGRKASSYGPREQ-GKYAAEFYTNVK 471
               FGG K S +G     G  +  FYT  K
Sbjct: 462 GAFSFGGWKKSLFGDTHMYGPESFNFYTRRK 492


Lambda     K      H
   0.317    0.134    0.391 

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: 600
Number of extensions: 31
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: 477
Length of database: 513
Length adjustment: 34
Effective length of query: 443
Effective length of database: 479
Effective search space:   212197
Effective search space used:   212197
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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