GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Trichormus variabilis ATCC 29413

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::Q8VWZ1
         (503 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  315 bits (807), Expect = 2e-90
 Identities = 185/482 (38%), Positives = 272/482 (56%), Gaps = 13/482 (2%)

Query: 9   QLFIDGEWRVPILNKRIPNINPSTEN-IIGDIPAATKEDVDLAVDAAKRAISRKNGRDWS 67
           Q +I+G+W        + + NP+ ++ I+   P +  +D D AV AA++A        W 
Sbjct: 8   QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYG-----SWR 62

Query: 68  AASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEE 127
                 RA Y+  +   + + K+EL +L S + GKP+ EA  D+ + V C  Y AG    
Sbjct: 63  KVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRR 122

Query: 128 LDSKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPS 187
           L   Q  P  +P     +  ++ PIGV ALITPWN+P  +  WK  PAL  G   ILKP+
Sbjct: 123 LFG-QTTPSEMPNKF--AMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPA 179

Query: 188 ELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIM 247
           E       +L EI    GLP GV+N+V G+G EAG +L  HP++D +SFTGSSATG+ + 
Sbjct: 180 EDTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVG 239

Query: 248 TTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIA 307
            T  +  K V LE+GGK+  VV ED DL+   +  ++G F T GQ C+ATSRLI+H  I 
Sbjct: 240 ETCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIK 299

Query: 308 VEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGR--R 365
            +F   L +    +++    E    +GPI++  Q ++V   ++ A+ EGA IL GG    
Sbjct: 300 EKFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359

Query: 366 PEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAV 425
              LK+GYF +PTI+ +VT  M++ REE+FGPV+A+   ST EEAI + NDT YGL S+V
Sbjct: 360 EGQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSV 419

Query: 426 MSNDLERCERLSKALQAGIVWINCAQ-PSFIQAPWGGIKRSGFG-RELGEWGLENYLSVK 483
            + D+ R     + ++ GI +IN     + +  P+GG+K++G G RE G   L+ +   K
Sbjct: 420 YTRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWK 479

Query: 484 QV 485
            V
Sbjct: 480 SV 481


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: 605
Number of extensions: 29
Number of successful extensions: 4
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: 498
Length adjustment: 34
Effective length of query: 469
Effective length of database: 464
Effective search space:   217616
Effective search space used:   217616
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 Apr 09 2024. 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