GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfacinum infernum DSM 9756

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_178371896.1 BUB04_RS04110 aldehyde dehydrogenase family protein

Query= BRENDA::P49189
         (494 letters)



>NCBI__GCF_900129305.1:WP_178371896.1
          Length = 481

 Score =  311 bits (798), Expect = 2e-89
 Identities = 186/457 (40%), Positives = 258/457 (56%), Gaps = 11/457 (2%)

Query: 33  EPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARIIREREDEIA 92
           +PATG+VIA      ++ V+ AV  A  A   W+      R  +LLE AR +  R D+++
Sbjct: 30  DPATGQVIARVPLCNDQVVDKAVAGALRAQPSWADAPVEHRTSLLLEWARAVSSRLDQLS 89

Query: 93  TMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAGEHIQLPG--GSFGYTRREPLGVC 150
            + C   GK +  AR +++ + Q + Y+A  A  + G H+ L G  GS     REP+GV 
Sbjct: 90  LLNCRETGKPLHAARAEVENAVQLIHYFAEEARRLTG-HLPLTGQPGSQTLVFREPVGVV 148

Query: 151 VGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGVPPGLFNVVQ 210
             I  +NYP      K+ PALA G A+V KP   TP++ L LA +  EAG+PPG+F VV 
Sbjct: 149 AAITPFNYPISTLVTKATPALAVGCAVVAKPDEHTPLATLELARLAEEAGLPPGVFQVVT 208

Query: 211 G-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPLIIFSDCDM 269
           G G  TG+ L  HP VA V+FTGS   G  I +++A G+K + LELGG  P I+  D D 
Sbjct: 209 GPGPETGRALAAHPKVALVTFTGSTEVGKFIQKLAADGVKRLILELGGHCPAILCRDADW 268

Query: 270 NNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPLLEDTRMGP 329
              +   L   F   GQ C   TR++V +EI D   E++      +K GDP   +T +GP
Sbjct: 269 VRLLPSILSQAFKNSGQYCYRITRLYVAREIWDAVLEKLTSAAATLKAGDPRDPETDLGP 328

Query: 330 LINRPHL-ERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNCRDDMTCV 388
           L N PH+ +RV   V+ A  QGA +  GG       P    G Y  P VLT+ R  M  +
Sbjct: 329 L-NNPHIFDRVRKQVQKALSQGAALALGGP-----PPGKDSGLYFPPTVLTDLRPGMDIL 382

Query: 389 KEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAGTCFINNY 448
           +EEIFGPV+ +L F  E E ++ ANDT FGLAA VF  D+ RA R+   +QAG+ +IN+ 
Sbjct: 383 REEIFGPVLLVLPFSDEQEAVDGANDTPFGLAAYVFCGDLSRALRMAHRIQAGSVWINDI 442

Query: 449 NVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCV 485
           + +  E PFGG K+SG GRE  R  +E +++LKT+ V
Sbjct: 443 HQARPEAPFGGMKQSGLGREKSRFGVEAFTELKTIYV 479


Lambda     K      H
   0.320    0.137    0.411 

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: 585
Number of extensions: 26
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: 494
Length of database: 481
Length adjustment: 34
Effective length of query: 460
Effective length of database: 447
Effective search space:   205620
Effective search space used:   205620
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 Apr 09 2024. 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