GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_255
          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:

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