GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Shewanella sp. ANA-3

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= BRENDA::Q97UA1
         (478 letters)



>lcl|FitnessBrowser__ANA3:7025959 Shewana3_3107
           methylmalonate-semialdehyde dehydrogenase [acylating]
           (RefSeq)
          Length = 496

 Score =  266 bits (680), Expect = 1e-75
 Identities = 154/451 (34%), Positives = 241/451 (53%), Gaps = 8/451 (1%)

Query: 33  KIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEFALLMTLEEGK 92
           ++ L ++D+V  AI  A + FD WS+     R  +L K   L+EQ   E A L+TLE GK
Sbjct: 33  QVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRARVLFKFKALVEQHMDELAQLITLEHGK 92

Query: 93  TLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVVALITPWNFPL 152
            L D+  E+ R   +++F   +   + G+           ++V + LGVVA I P+NFP+
Sbjct: 93  VLDDARGELIRGLEVVEFACGIPHLLKGEHTEQVGGGVDAWSVNQALGVVAGIAPFNFPV 152

Query: 153 SIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVVGKGSEVGDTI 212
            +P+W    A+A GNT ++KP+ K P  V ++ E+L++AGLP GV N+V G   E  DT+
Sbjct: 153 MVPMWMFPIAIACGNTFIMKPSEKDPSAVMRIAELLTQAGLPAGVFNVVNG-DKEAVDTL 211

Query: 213 VSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLTLAAELAV 272
           +S ++I AVSF GST + + IY       +  R+Q   G KN + +   ADL  A    +
Sbjct: 212 LSHEDIQAVSFVGSTPIAEYIYSTASKHGK--RVQALGGAKNHMLLMPDADLDQAVSALM 269

Query: 273 RGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPG-TEDVDMGPVVDEGQFK 331
              +G  G+ C A S ++   DV  +   +LL ++++ +VG G T +++MGP++      
Sbjct: 270 GAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQIQQLKVGNGLTPEMEMGPLISRQHLA 329

Query: 332 KDLEYIEYGKNVGAKLIYGGNIIP----GKGYFLEPTIFEGVTSDMRLFKEEIFGPVLSV 387
           K  E+++ G   GA L+  G  +      +GYFL   +F+ VT +MR+++EEIFGPVLS+
Sbjct: 330 KVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLGACLFDNVTPEMRIYREEIFGPVLSI 389

Query: 388 TEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLELQAPFG 447
              KD   A+ L+N  ++G+   I     +A   F   V+ G++ VN P         FG
Sbjct: 390 VRVKDYASALALINQHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFG 449

Query: 448 GFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478
           G+K S        G D + FY K K +   W
Sbjct: 450 GWKRSLFGPLHMHGPDGVRFYTKRKAITARW 480


Lambda     K      H
   0.316    0.135    0.389 

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: 566
Number of extensions: 37
Number of successful extensions: 7
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: 478
Length of database: 496
Length adjustment: 34
Effective length of query: 444
Effective length of database: 462
Effective search space:   205128
Effective search space used:   205128
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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