GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Acidovorax sp. GW101-3H11

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Ac3H11_255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_255 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 478

 Score =  371 bits (952), Expect = e-107
 Identities = 194/469 (41%), Positives = 280/469 (59%), Gaps = 2/469 (0%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKE 71
           Q FI G W DA  G+T+ V NPATG+ +G V      +  RA++AA K   AWR + A E
Sbjct: 7   QLFIAGQWQDAVEGKTLAVFNPATGKEIGRVAHATKVDLDRALDAAQKGFEAWRDIPAAE 66

Query: 72  RATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVI 131
           RA  +RR   L+ E  + +A +M  EQGKPLAEAK E + +A  IEWFA+E+ R+YG ++
Sbjct: 67  RAKTMRRAAALMRERAEAIAAIMVQEQGKPLAEAKVETMASADIIEWFADESLRVYGRIV 126

Query: 132 PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA 191
           P      + +V+K P+G  AA TPWNFP   + RK   ALAAGC++++K   +TP S   
Sbjct: 127 PSRNLKAQQMVLKDPVGPVAAFTPWNFPINQVVRKLAAALAAGCSILVKAPEETPASPAE 186

Query: 192 LAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKK 251
           L      AG+P G   +V G   +I S L  +PI+RK++FTGST +G+QL +   K +K+
Sbjct: 187 LIRAFADAGVPVGTVGLVYGDPAEISSYLIPHPIIRKVTFTGSTPVGKQLAALAGKHMKR 246

Query: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKV 311
           V++ELGG+AP IV +DADL+ A++ +  +K+RN GQ C+   R  + + +   F      
Sbjct: 247 VTMELGGHAPVIVAEDADLELAIKISSGAKFRNAGQVCISPTRYLVHENIRADFVAGFAK 306

Query: 312 AVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPT 369
               LK+G+GL AGT  GPL + + +  + + +ADA+ +GA VLAGG+ +  EGNFF PT
Sbjct: 307 YAQGLKVGDGLTAGTQMGPLANPRRITAMADLLADAVQQGAKVLAGGERIGSEGNFFAPT 366

Query: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAE 429
           +L +VP +A +  EE FGP+A +  F    D IA +N   FGLA Y +   L     +A+
Sbjct: 367 VLNDVPLSARIVNEEPFGPVAAVRGFTKIEDAIAEANRLPFGLAGYAFTTSLKNAHLLAQ 426

Query: 430 ALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
            LE GM+ +N         PFGG+K SG G EG    IE ++  + + +
Sbjct: 427 RLEVGMLWINQAAAPAAELPFGGLKDSGYGSEGGPEAIEAHMNTRLVSI 475


Lambda     K      H
   0.317    0.135    0.390 

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: 601
Number of extensions: 27
Number of successful extensions: 2
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: 480
Length of database: 478
Length adjustment: 34
Effective length of query: 446
Effective length of database: 444
Effective search space:   198024
Effective search space used:   198024
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: 51 (24.3 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 paper from 2022 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