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_612 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_612
          Length = 483

 Score =  270 bits (691), Expect = 6e-77
 Identities = 174/477 (36%), Positives = 237/477 (49%), Gaps = 12/477 (2%)

Query: 8   HYINGHKTNGVADSHQEVTNPA-TGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIR 66
           H ING    G        TNP+ T +V  + A A +   + AV AA  A P WS + P R
Sbjct: 12  HLINGRWEIGTTTGIS--TNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQR 69

Query: 67  RARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYT 126
           RA V+      L A KDEL   + RE GK   +   EVAR   I +F  G    ++G+  
Sbjct: 70  RADVLDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELL 129

Query: 127 EQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLM 186
             V  G+    TR+P+GVV  I P+NFP  +P W    A+A GN+ V KP+ L P+    
Sbjct: 130 ASVRQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWA 189

Query: 187 MADLLKQAGLPDGVFNVVQGDKDSV-EALIDHPDVKALSFVGSTPIANLIYERGARSGKR 245
           +A+++ ++GLP G FN++ G    V + L+DHP V ALSF GS    + I    ++   +
Sbjct: 190 LAEIISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAK 249

Query: 246 IQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAE 305
           +Q   G KN ++V+ DA+LD+AVD  +  +Y S G+RC A S  ++  +V D  V RL  
Sbjct: 250 VQLEMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRN 309

Query: 306 RARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCA 365
           R   LK+ + LE   EMGP+V      +  GYI+   +EGAE V  G   +    G    
Sbjct: 310 RLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGH--- 366

Query: 366 DGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESG 425
              +M   LF    PE  + REEIFGPV   +R  D   A+ L ND  FG      T S 
Sbjct: 367 ---YMSPALF-LARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSL 422

Query: 426 SVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482
             A  F R   VGM  +N+P         FGG K S +G     G     FYT  K+
Sbjct: 423 KRAMHFKRHAAVGMTMVNLPTAGVDFHVPFGGRKESSYG-AREQGRYAAEFYTTVKT 478


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: 603
Number of extensions: 34
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: 483
Length adjustment: 34
Effective length of query: 469
Effective length of database: 449
Effective search space:   210581
Effective search space used:   210581
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