GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas stutzeri RCH2

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases

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



>lcl|FitnessBrowser__psRCH2:GFF882 Psest_0905 NAD-dependent aldehyde
           dehydrogenases
          Length = 499

 Score =  320 bits (821), Expect = 5e-92
 Identities = 183/474 (38%), Positives = 270/474 (56%), Gaps = 9/474 (1%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           FID  WV  + G+T+ + NPA G+IL  +P   AA+  RA++AA +A   WR  +  ERA
Sbjct: 20  FIDNQWVSDEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFMTWRTTSPAERA 79

Query: 74  TKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGDVIP 132
             L +  +L+  + D  A L TL+ GKP+ E++  +I  A     +FA    R   D   
Sbjct: 80  NALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVI-RSQSDEAV 138

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192
                   I + +P+GV   + PWNFP  M   K  PA+AAG T+V+KP+  TP +   L
Sbjct: 139 MLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTILEL 198

Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252
           A++  +  +PAGV ++V+G    +G  L  +P +RKL+FTGST +G  + +  AK I   
Sbjct: 199 AKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKIIPA 257

Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312
           +LELGG +  IVF DA+ DKAVEGA+++   N GQ C    RL++ + +Y+ F  +LK  
Sbjct: 258 TLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAELKHK 317

Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPMEGN------FF 366
              +++G+ L   T  G  + +  + ++  ++  A  +GA VL GG  + G       F 
Sbjct: 318 FEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTGANYDAGFFI 377

Query: 367 EPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR 426
           +PTIL  V N+  VA EE FGP+  +  FKDEA+VIAM+ND+E+GLA   + +D+ R  R
Sbjct: 378 QPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINRALR 437

Query: 427 VAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
           VA A+E G + VNT       APFGG K SGLGRE  K  +E Y + K + + +
Sbjct: 438 VARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 491


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: 573
Number of extensions: 33
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: 499
Length adjustment: 34
Effective length of query: 446
Effective length of database: 465
Effective search space:   207390
Effective search space used:   207390
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