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

GapMind for catabolism of small carbon sources

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

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q8VWZ1
         (503 letters)



>lcl|FitnessBrowser__Cola:Echvi_1497 Echvi_1497 NAD-dependent
           aldehyde dehydrogenases
          Length = 469

 Score =  174 bits (440), Expect = 8e-48
 Identities = 127/422 (30%), Positives = 204/422 (48%), Gaps = 13/422 (3%)

Query: 72  SLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSK 131
           S R + L  +   IK  + E+ K    D  KP  E +A  +      E  A L +     
Sbjct: 22  SSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAE-VAVTETSFVVMEINAALKQLPKWT 80

Query: 132 QKAPISLPMDTF--KSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189
               +  P+     ++Y+  EP G V +I+PWNYPF ++   +  A+AAGC+A LKPSE 
Sbjct: 81  APTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEH 140

Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249
           +  T   L  +  E+     V  I  G G    + L   P  D I FTGS+  G  +M  
Sbjct: 141 SPHTSALLRRMVTELFAVEDV-TIFEG-GVPVTSELLEQP-FDHIFFTGSTEVGKIVMKA 197

Query: 250 AAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVE 309
           AA+ +  V+LELGGKSP ++ +  DL+  A+    G F  +GQ C A   L VHES   +
Sbjct: 198 AAKNLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQD 257

Query: 310 FVDKLVKWAENIKISD--PLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPE 367
           F++ L      +  ++    +     G I+      ++ N +  A+++GA +  GG+   
Sbjct: 258 FIETLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGKNSL 317

Query: 368 HLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMS 427
             +   F+EPT++++V+ +M + +EE+FGP+L + T+   ++ I L       L     +
Sbjct: 318 DQQ---FMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFT 374

Query: 428 NDLERCERLSKALQAGIVWINCAQPSFI--QAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
            D    E+LSK   +G + IN     F+  + P+GGI  SG GR  G  G   + + K +
Sbjct: 375 TDDRIIEQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAI 434

Query: 486 TR 487
            +
Sbjct: 435 LK 436


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: 454
Number of extensions: 22
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: 469
Length adjustment: 34
Effective length of query: 469
Effective length of database: 435
Effective search space:   204015
Effective search space used:   204015
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 Sep 17 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources