GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Acidovorax sp. GW101-3H11

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1496
          Length = 500

 Score =  348 bits (893), Expect = e-100
 Identities = 196/472 (41%), Positives = 280/472 (59%), Gaps = 12/472 (2%)

Query: 19  PILNKR-IPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARY 77
           P L+ R +P  +P+TE ++ + P +   D+  AV +A+RA    +   W     + R + 
Sbjct: 32  PALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAF---DSHVWRGLRPADREKL 88

Query: 78  LRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFE---YYAGLAEELDSKQ-K 133
           L  ++  I+   DEL  LE++  GK   + +A   DV A  E   Y AG A +L+ +   
Sbjct: 89  LFRLSELIERHADELSALETLQSGKL--QGIARAIDVQAGAEFVRYMAGWATKLEGQTLD 146

Query: 134 APISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVT 193
             I +P   + +Y  +EP+GVV  I PWN+P  +A WKIAPALAAGC  +LKPSE   +T
Sbjct: 147 NSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLT 206

Query: 194 CLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQL 253
            L L  +  E G+P GVLN+V G G  AGA+L +HP V K+SFTGS+A G  +   A + 
Sbjct: 207 ALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHAAVEN 266

Query: 254 VKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDK 313
           +   +LELGGKSP VV ED D  +VA+    G FF  GQ+C+A+SRL+VH S+    +D+
Sbjct: 267 MARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLDE 326

Query: 314 LVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGY 373
           L   A+ ++I    +   + GP+ S+A + +V++ I+SAK+EGAT++ GG R      G 
Sbjct: 327 LAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERVH--DAGC 384

Query: 374 FVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERC 433
           FV+PTI  D T  M++ REEVFGPVLAV  F   E+AI  ANDT YGL +++ +  L   
Sbjct: 385 FVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHA 444

Query: 434 ERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
            R+   LQAG+VW+N         P GGIK+SG GR+LG   +E +  +K V
Sbjct: 445 HRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496


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: 524
Number of extensions: 20
Number of successful extensions: 2
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: 500
Length adjustment: 34
Effective length of query: 469
Effective length of database: 466
Effective search space:   218554
Effective search space used:   218554
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.

Links

Downloads

Related tools

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