GapMind for catabolism of small carbon sources

 

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

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= reanno::Smeli:SM_b20891
         (477 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3961
          Length = 512

 Score =  674 bits (1739), Expect = 0.0
 Identities = 341/481 (70%), Positives = 391/481 (81%), Gaps = 8/481 (1%)

Query: 3   LHQNLIAGEWVGGDGVA---NINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59
           +H NLI G W   DGV    N NPS+T DV+G+YA AS E A  A+AAA AAFPAWS S 
Sbjct: 34  MHANLIGGAWT--DGVRTYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLST 91

Query: 60  ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119
             +R  IL    +EI+ARK ELG LL+REEGKTL E IGE  RA  IF+FFAGE LR  G
Sbjct: 92  PQQRFDILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGG 151

Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179
           EV+PSVRPG+G+EITREP G +GIITPWNFPIAIPAWK+APAL YGN +VFKPAE+VPG 
Sbjct: 152 EVMPSVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGS 211

Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239
           +WA+ DILHRAGLP GV NLVMG+GS VG  +L+   +  ++FTGS  TG+RVA A V  
Sbjct: 212 AWALADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPR 271

Query: 240 NRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299
             K QLEMGGKNPFVVLDDADL+VAV AA+NS FFSTGQRCTASSR+IVTEGIHDRFVAA
Sbjct: 272 GAKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAA 331

Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRD---T 356
           M E++K L VDDA K GT IGPVVD  QL QD +YI IG+QEGAKLA+GGE + ++    
Sbjct: 332 MVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADGA 391

Query: 357 PGFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSL 416
           PGFYL+PALFTE T  MRI+REEIFGPV +V+R K+Y+EALA+ANDTPFGL+SGIATTSL
Sbjct: 392 PGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSL 451

Query: 417 KHATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTL 476
           KHATHFKR+A+AGMVMVNLPTAGVD+HVPFGGRK+SSYGPREQG+YAAEFYT VKTAYT 
Sbjct: 452 KHATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYGPREQGRYAAEFYTTVKTAYTQ 511

Query: 477 A 477
           A
Sbjct: 512 A 512


Lambda     K      H
   0.317    0.134    0.391 

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: 815
Number of extensions: 32
Number of successful extensions: 3
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: 477
Length of database: 512
Length adjustment: 34
Effective length of query: 443
Effective length of database: 478
Effective search space:   211754
Effective search space used:   211754
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 (21.7 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