GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF882
          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:

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