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_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q8VWZ1
         (503 letters)



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

 Score =  333 bits (855), Expect = 7e-96
 Identities = 194/485 (40%), Positives = 290/485 (59%), Gaps = 22/485 (4%)

Query: 11  FIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAAS 70
           FI G++  P+  +    I+P    +   +      D++LA+DAA +A        WS  S
Sbjct: 25  FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA-----WSRTS 79

Query: 71  GSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEAL-ADLDDVVACFEYYAGLAEELD 129
            + R+  L  IA +I+ K + L  +E+ID GKP+ E + ADL  VV  F Y+AG+   + 
Sbjct: 80  ATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGV---IR 136

Query: 130 SKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189
           +++ +   L   T  S  +KEPIG+V  I PWN+P LMATWK+APALAAGC  I+KP+E 
Sbjct: 137 AEEGSIAELDQHTV-SVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQ 195

Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249
              + + L E+  ++ LP GVLN+V G G EAG  LA  P +DK++FTG + TG  IM  
Sbjct: 196 TPASIMILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQY 254

Query: 250 AAQLVKPVSLELGGKSPIVVF------EDVDLDKVAEWTVFGCFFTNGQICSATSRLIVH 303
           A++ + PV++ELGGKSP V F      +D  LDK  E  V       G++C+  SR++VH
Sbjct: 255 ASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFAL-NQGEVCTCPSRILVH 313

Query: 304 ESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG 363
           E I   F++K++  AE I++  PL++   +G   S+ Q++K+L+ I   K EGA +LTGG
Sbjct: 314 EKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGG 373

Query: 364 ---RRPEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYG 420
              +    L+ GY+V+PT++      M++++EE+FGPV +V TF   EEAI+++NDT YG
Sbjct: 374 EVAKLNSGLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYG 432

Query: 421 LGSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYL 480
           LG+ V + D     ++ +A++AG VW+NC       AP+GG K+SGFGRE     L +Y 
Sbjct: 433 LGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYR 492

Query: 481 SVKQV 485
             K +
Sbjct: 493 QNKNM 497


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: 599
Number of extensions: 21
Number of successful extensions: 7
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: 509
Length adjustment: 34
Effective length of query: 469
Effective length of database: 475
Effective search space:   222775
Effective search space used:   222775
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:

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