GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dyella japonica UNC79MFTsu3.2

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0379
          Length = 476

 Score =  181 bits (458), Expect = 7e-50
 Identities = 139/458 (30%), Positives = 216/458 (47%), Gaps = 27/458 (5%)

Query: 21  DVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQLLEANEE 80
           DV +  +G+   +V + D +  +QAI AA  A    R   P +R  VL    Q      +
Sbjct: 22  DVLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERRD 81

Query: 81  RIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE-YSRNVGPNIDAWSDFQ-- 137
            +   +  E GK I+D+AGE+ R IE    A        GE  +  +   ++ +  +   
Sbjct: 82  ELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRR 141

Query: 138 -PIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAGLPKG 196
            P+G V+ ITPFNFP  +       AIA G  F+LKP+ER P   L+I E+  E  LPKG
Sbjct: 142 VPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKG 201

Query: 197 VLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAKNHAVLM 256
             ++++ D      L+E P  K LSF GS    +     G K  K    LGG   +A  +
Sbjct: 202 AFSILNLDGKHASPLVEDPRFKLLSFTGSQIGWDLKTRAGHK--KVTLELGG---NAACI 256

Query: 257 PDAD----LDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKIGA 312
            DAD    LD+ +  L+  A+   G+ C+++   +   + + D L ++LV  +KGLK G 
Sbjct: 257 VDADQLPRLDHVIERLVFGAFYQSGQSCISVQ-RIYAHESLYDELKKRLVAAVKGLKAGD 315

Query: 313 GTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFDRV 372
                  +GP++  AA +++ G+I+     G +++  G+         G  L  TL + V
Sbjct: 316 PKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGK-------RKGPMLEATLMENV 368

Query: 373 TPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVG 432
             +  + ++E+FGP   +    SL+EA+ + ND +YG    IFT     A    +E+E G
Sbjct: 369 RGDAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQG 428

Query: 433 MVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRF 470
            V VN      V    +GG K      L   G +GVR+
Sbjct: 429 GVIVNDVPSFRVDNMPYGGVK------LSGAGREGVRY 460


Lambda     K      H
   0.319    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: 568
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: 498
Length of database: 476
Length adjustment: 34
Effective length of query: 464
Effective length of database: 442
Effective search space:   205088
Effective search space used:   205088
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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