GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas putida KT2440

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate PP_2487 PP_2487 putative aldehyde dehydrogenase

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



>lcl|FitnessBrowser__Putida:PP_2487 PP_2487 putative aldehyde
           dehydrogenase
          Length = 503

 Score =  322 bits (825), Expect = 2e-92
 Identities = 184/474 (38%), Positives = 271/474 (57%), Gaps = 9/474 (1%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           FID  WV A+ G+T+ + NPA G+IL  +P   AA+  RA++AA +A   WR  +  ERA
Sbjct: 24  FIDNQWVTAEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFVTWRTTSPAERA 83

Query: 74  TKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGDVIP 132
             L +  +L+  + D  A L TL+ GKP+ E++  +I  A     +FA    R   D   
Sbjct: 84  NALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVI-RSQSDEAV 142

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192
                   I + +P+GV   + PWNFP  M   K  PA+AAG T+V+KP+  TP +   L
Sbjct: 143 MLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTILEL 202

Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252
           A++  +  +PAGV ++V+G    +G  L  +P +RKL+FTGST +G  + +  AK I   
Sbjct: 203 AKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKIIPA 261

Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312
           +LELGG +  IVF DA+ DKAVEGA+++   N GQ C    RL++ + +Y+ F  +LK  
Sbjct: 262 TLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAELKHK 321

Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPMEGN------FF 366
              +++G+ L   T  G  + +  + ++  ++  A  +GA VL GG  + G       F 
Sbjct: 322 FEAVRVGDPLNPDTMMGAQVSKTQMERILGYVDIAKEEGAEVLIGGGRLTGADYDAGFFI 381

Query: 367 EPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR 426
           +PTIL  V N+  VA EE FGP+  +  FKDEA+VIAM+ND+E+GLA   + +D+ R  R
Sbjct: 382 QPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINRALR 441

Query: 427 VAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
           VA A+E G + VNT       APFGG K SGLGRE  K  +E Y + K + + +
Sbjct: 442 VARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 495


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: 571
Number of extensions: 35
Number of successful extensions: 5
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: 503
Length adjustment: 34
Effective length of query: 446
Effective length of database: 469
Effective search space:   209174
Effective search space used:   209174
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: 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 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