GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_0481
          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:

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