GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__Cola:Echvi_0481 Echvi_0481 NAD-dependent
           aldehyde dehydrogenases
          Length = 509

 Score =  254 bits (648), Expect = 6e-72
 Identities = 151/475 (31%), Positives = 254/475 (53%), Gaps = 15/475 (3%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +I G+FV      + DV++P    V +++  G+A D   A+DAA +A P W    A ER+
Sbjct: 25  FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATERS 84

Query: 70  SWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
           + L KI+  I  +   ++A+   + GK +++    ++A   D+  Y A   R  EG I +
Sbjct: 85  NILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIAE 144

Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188
            D+   ++ + K  +G+   I+PWNFP  +   KMAPAL  G   ++KP+E TP + +  
Sbjct: 145 LDQHTVSVNV-KEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMIL 203

Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
            +++ ++ LP GV N+V G G   G+ LA +P++  V+ TG  + G  IM  A++N+  V
Sbjct: 204 MEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNPV 262

Query: 249 CLELGGKAPAIVMD---DADLELAVKAIVDSRV--INSGQVCNCAERVYVQKGIYDQFVN 303
            +ELGGK+P +      DAD E   K +  + +  +N G+VC C  R+ V + IYD F+ 
Sbjct: 263 TMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDAFME 322

Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVE---- 359
           ++    +A+Q G+P ++  + MG   +    E++   +    +EGA V  GG+  +    
Sbjct: 323 KVIARAEAIQMGHPLDKTTM-MGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNSG 381

Query: 360 -GKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQ 418
              GYY  PTLL     +M +  EE FGPV  V  F  +E+AIS++ND+ YGL + ++T+
Sbjct: 382 LENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTR 440

Query: 419 NLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473
           + + A +  + +K G  ++N  +         G++KSG G       L+ Y Q +
Sbjct: 441 DAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNK 495


Lambda     K      H
   0.318    0.135    0.392 

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: 550
Number of extensions: 34
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 479
Length of database: 509
Length adjustment: 34
Effective length of query: 445
Effective length of database: 475
Effective search space:   211375
Effective search space used:   211375
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 (21.7 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:

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 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