GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Desulfobacter vibrioformis DSM 8776

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  317 bits (813), Expect = 5e-91
 Identities = 186/480 (38%), Positives = 267/480 (55%), Gaps = 10/480 (2%)

Query: 30  QQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQL 89
           + P + C   FI ++W +A S+K     NP+TGEV+  V     ++  +A+ AA  +   
Sbjct: 5   KDPGLLCQACFIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA 64

Query: 90  GSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYY 149
              WR   A+ R  +L R  DL+  ++  LA L T + GKP   S   ++        ++
Sbjct: 65  ---WRSKTAAQRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESR-GEIAYAASFFEWF 120

Query: 150 AGWADKYHGKTIP--IDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVV 207
           A  A + +G  IP  I        + +PVGV   I PWNFP  M   K G ALA G  +V
Sbjct: 121 AEEAKRIYGDIIPQTIASQRLVVIK-QPVGVVAAITPWNFPSAMITRKAGAALAAGCTMV 179

Query: 208 MKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG 267
           +K A  TP +AL +A L +EAG PPGV N+V G     G  + ++  V K+ FTGSTE+G
Sbjct: 180 VKPATATPFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVG 239

Query: 268 R-VIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTF 326
           + ++Q  AG+  +KRV++ELGG +P I+  DAD+D AVE A    + N GQ C   +R +
Sbjct: 240 KKLMQDCAGT--MKRVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLY 297

Query: 327 VQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLC 386
           VQ  +YD+F E+      +  VGN  +    QGP +D    + +  +IN    +GAK+L 
Sbjct: 298 VQAGVYDQFCEKLARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLA 357

Query: 387 GGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAA 446
           GG   A  G F  PTV  DV D M +AKEEIFGP   I KF++  EVV +AN++ YGLAA
Sbjct: 358 GGKRHALGGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAA 417

Query: 447 AVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506
             FT+D+ +   + + L+ G + +N   +  A +PFGG K SG+GRE  +YGL  Y E+K
Sbjct: 418 YFFTRDMARTWRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIK 477


Lambda     K      H
   0.319    0.136    0.409 

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: 591
Number of extensions: 28
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: 517
Length of database: 485
Length adjustment: 34
Effective length of query: 483
Effective length of database: 451
Effective search space:   217833
Effective search space used:   217833
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: 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