GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Sulfurimonas denitrificans DSM 1251

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  249 bits (635), Expect = 2e-70
 Identities = 152/456 (33%), Positives = 238/456 (52%), Gaps = 10/456 (2%)

Query: 29  KVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIENQD 88
           K  NP  GEV          + ++A+  A  A       T  +R + L      + +N++
Sbjct: 19  KRVNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKE 78

Query: 89  DLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTI--PGHQPDKRLIVI--K 144
           D+A+ +T E GKP+  ++ E+      +   AE  + ++G+T+        K+ I    +
Sbjct: 79  DIAKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSR 138

Query: 145 QPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIPA- 203
            P GV  AITP+NFP  +I  K  PAL AG  ++LKP  + P +A    +L   +     
Sbjct: 139 VPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIK 198

Query: 204 GVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPFI 263
             LSVV G A +VGG L  + + R +SFTGS  +G  + +     IKKVSLELGGNA   
Sbjct: 199 DALSVVYGDA-DVGGTLVTSEIPRVISFTGSVGVGEIITKSAG--IKKVSLELGGNAATF 255

Query: 264 VFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGLE 323
           +   A+LD A +   I  + N+GQ C+   RIYV   +Y  FA K+A A  KL +G+  E
Sbjct: 256 IDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE 315

Query: 324 EGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFEPTILVDVPKTAAVAKE 383
           E T  GPL++ +A  +  E ++ A+ +GA  +   + +EG  F P ++ DV +  A+  +
Sbjct: 316 EDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPR-VEGRVFYPCVMADVKEDMAIVCQ 374

Query: 384 ETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGIN-TGL 442
           E F P+  L   KD  E + M N++ +GL    +  D++   R    L+ G + IN    
Sbjct: 375 EVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMPT 434

Query: 443 ISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCI 478
           +  ++ P+GG+K SG+GREG ++ IE+  EIK + I
Sbjct: 435 LRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.317    0.134    0.384 

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: 513
Number of extensions: 19
Number of successful extensions: 6
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: 480
Length of database: 471
Length adjustment: 33
Effective length of query: 447
Effective length of database: 438
Effective search space:   195786
Effective search space used:   195786
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: 51 (24.3 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