GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Echinicola vietnamensis KMM 6221, DSM 17526

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Cola:Echvi_0481
          Length = 509

 Score =  370 bits (949), Expect = e-107
 Identities = 204/481 (42%), Positives = 288/481 (59%), Gaps = 16/481 (3%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  ++   V  + F  ++P  G+V  +VA G   D++ A+ AA  AF     W R  A+
Sbjct: 25  FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA---WSRTSAT 81

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +L ++AD IE    YLAA+ET+DNGKP   +   DL +V+   RY+AG      G 
Sbjct: 82  ERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGS 141

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              +D    S    EP+G+ GQIIPWNFP+LM  WK+ PALA G   ++K AEQTP + +
Sbjct: 142 IAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIM 201

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +  +I +   P GV+N+V GFGP AG  +A    +DKVAFTG T  GR+I   A S NL
Sbjct: 202 ILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYA-SENL 259

Query: 280 KRVTLELGGKSPNII---MSDADMDWAVEQAHFALFF--NQGQCCCAGSRTFVQEDIYDE 334
             VT+ELGGKSPN+    + DAD ++  +    A+ F  NQG+ C   SR  V E IYD 
Sbjct: 260 NPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDA 319

Query: 335 FVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA--- 391
           F+E+ +ARA++  +G+P D  T  G Q  + QF+KIL YI+ GKQEGA++L GG +A   
Sbjct: 320 FMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLN 379

Query: 392 --ADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVF 449
              + GY+++PT+     + M + +EEIFGPV  +  FK +EE +  +N++ YGL A V+
Sbjct: 380 SGLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVW 438

Query: 450 TKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVT 509
           T+D  +A  + +A++AG VWVNCY  + A +PFGGYK SG GRE     L  Y + K + 
Sbjct: 439 TRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNML 498

Query: 510 V 510
           +
Sbjct: 499 I 499


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: 659
Number of extensions: 40
Number of successful extensions: 6
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: 509
Length adjustment: 35
Effective length of query: 482
Effective length of database: 474
Effective search space:   228468
Effective search space used:   228468
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 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