GapMind for catabolism of small carbon sources

 

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

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= metacyc::MONOMER-15203
         (503 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3961
          Length = 512

 Score =  265 bits (677), Expect = 3e-75
 Identities = 170/475 (35%), Positives = 242/475 (50%), Gaps = 8/475 (1%)

Query: 10  INGHKTNGVADSHQEVTNPA-TGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRA 68
           I G  T+GV       TNP+ T  V G  A+AS+     AVAAA AAFPAWS + P +R 
Sbjct: 39  IGGAWTDGVRTYQN--TNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRF 96

Query: 69  RVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQ 128
            ++      + A K EL + + RE GK   +A GEV R   I +F  G      G+    
Sbjct: 97  DILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGGEVMPS 156

Query: 129 VSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMA 188
           V  G+    TR+PLG +  ITP+NFP+ +P W    A+A GN  V KP+ + P ++  +A
Sbjct: 157 VRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWALA 216

Query: 189 DLLKQAGLPDGVFNVVQGDKDSVEA-LIDHPDVKALSFVGSTPIANLIYERGARSGKRIQ 247
           D+L +AGLP GVFN+V G    V A L++   +  +SF GS      +       G ++Q
Sbjct: 217 DILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPRGAKVQ 276

Query: 248 ALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERA 307
              G KN  VV+ DA+L+ AV A I + + S G+RC A S  ++   + D+ V  + E+ 
Sbjct: 277 LEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAAMVEKM 336

Query: 308 RDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADG 367
           + LK+ +  +   ++GP+V  +   +   YI  G  EGA++   G   + +  G   A G
Sbjct: 337 KTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADG---APG 393

Query: 368 FWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSV 427
           F++   LF   TP M I REEIFGPV++ +R  +   A+ L ND  FG      T S   
Sbjct: 394 FYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSLKH 453

Query: 428 AREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482
           A  F R  Q GMV +N+P         FGG K S +G     G     FYT  K+
Sbjct: 454 ATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYG-PREQGRYAAEFYTTVKT 507


Lambda     K      H
   0.319    0.136    0.406 

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: 645
Number of extensions: 33
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: 503
Length of database: 512
Length adjustment: 34
Effective length of query: 469
Effective length of database: 478
Effective search space:   224182
Effective search space used:   224182
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 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:

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