GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Echinicola vietnamensis KMM 6221, DSM 17526

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__Cola:Echvi_3822
          Length = 453

 Score =  246 bits (629), Expect = 9e-70
 Identities = 146/463 (31%), Positives = 249/463 (53%), Gaps = 19/463 (4%)

Query: 27  NINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIK 86
           +INP T  ++ +    T++ V+ A+   + A        W     S RA  ++     ++
Sbjct: 3   SINPYTGELLEEFTDHTEQQVEAAIQKGQEAYL-----SWRELPISQRADLMKKAGQVLR 57

Query: 87  EKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSKQKAPISLPMDTFKSY 146
           +  D+ GK+ S++ GK + E+ ++++      EYYA  AEE+ +   API+LP D  ++ 
Sbjct: 58  DNTDKYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLAD--APIALP-DGKEAK 114

Query: 147 ILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEVGL 206
           ++  P+G+V  + PWN+PF       AP L AG   +LK +       L + E+  + G 
Sbjct: 115 VVYNPLGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGF 174

Query: 207 PRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGKSP 266
           P GV   +  +G +  A++ +HPDV   + TGS   G KI   A + +K   LELGG  P
Sbjct: 175 PEGVFQSLL-IGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDP 233

Query: 267 IVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKISDP 326
            +V +D D+ + A+    G     GQ C A  R I+ + +  EF+       E+    DP
Sbjct: 234 FIVLKDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDP 293

Query: 327 LEE----GCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGYFVEPTIITD 382
           L+E     C   P ++   Y++V     ++  +GA ++  G +PE  K   F++P I+  
Sbjct: 294 LDEKAGYACMARPDLAMELYEQV----EASIQKGAEVILEGTKPEKGKA--FIKPYILGK 347

Query: 383 VTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKALQA 442
           +T  M  +REE+FGPV +V   +  +EAI +AND+ +GLG+++ + D ++ + LS+ +++
Sbjct: 348 LTPDMPAYREELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIES 407

Query: 443 GIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
           G V+IN    S    P+GGIK+SG+GREL E G++ ++++K V
Sbjct: 408 GAVFINSMVASNPYLPFGGIKKSGYGRELAENGIKEFMNIKTV 450


Lambda     K      H
   0.317    0.134    0.402 

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: 507
Number of extensions: 19
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: 503
Length of database: 453
Length adjustment: 34
Effective length of query: 469
Effective length of database: 419
Effective search space:   196511
Effective search space used:   196511
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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