GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Sulfurimonas denitrificans DSM 1251

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  189 bits (481), Expect = 1e-52
 Identities = 138/467 (29%), Positives = 234/467 (50%), Gaps = 28/467 (5%)

Query: 40  LSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVE 99
           ++P +G   ++  +C+  DA +A+  A         S+   A+R + L+  A  L +N E
Sbjct: 21  VNPYNGEVASEFVTCNADDAKKALNIALLASKEA--SKTTIAQRCSWLLDVASKLAQNKE 78

Query: 100 ELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVT----- 154
           ++A   T ++GKPI   S I++    + +   AE +  ++ E   T     G  T     
Sbjct: 79  DIAKTITDEVGKPI-TYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFS 137

Query: 155 REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIP- 213
           R P GVV AI P+NFPL +   K+ PAL  GN+V+LKP+ ++PLTA + A+L IE+    
Sbjct: 138 RVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAI 197

Query: 214 AGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSP 273
              L+V+ G    VG  L        + FTGS  + + +   AG   +K++ LE GG + 
Sbjct: 198 KDALSVVYG-DADVGGTLVTSEIPRVISFTGSVGVGEIITKSAG---IKKVSLELGGNAA 253

Query: 274 NIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGN 333
             +   A +L  AA+  A     N G+VC +  R+ V + I  +F   + EA K    G+
Sbjct: 254 TFIDKSA-NLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGS 312

Query: 334 PLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTN 393
           P +  T +G LV+ +     + ++++  K+GA  +   +       G    P +   V  
Sbjct: 313 PYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPR-----VEGRVFYPCVMADVKE 367

Query: 394 AMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSV 453
            M I  +E+F P++S+I     +EA+ + N++PYGL   I+T+D++   +    + AG +
Sbjct: 368 DMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGI 427

Query: 454 WVN-----QYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495
            +N     ++D      P+GG K SG GR+    A+E+ +E+K+  I
Sbjct: 428 VINDMPTLRFD----IQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.316    0.132    0.390 

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: 495
Number of extensions: 31
Number of successful extensions: 4
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: 497
Length of database: 471
Length adjustment: 34
Effective length of query: 463
Effective length of database: 437
Effective search space:   202331
Effective search space used:   202331
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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