GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas stutzeri RCH2

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__psRCH2:GFF374
          Length = 480

 Score =  365 bits (938), Expect = e-105
 Identities = 200/480 (41%), Positives = 281/480 (58%), Gaps = 6/480 (1%)

Query: 1   MKSYQGLADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTP 60
           ++ Y    D    GS     + NP+D   V+ +        V++AI  A   F  W+   
Sbjct: 4   VQRYDNFIDGQWVGSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWATFG 63

Query: 61  APKRGSILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISG 120
              R   L K G  +    +E   L+  EEGKTL +++ EV R+ N+ K++     + +G
Sbjct: 64  IQARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLRQAG 123

Query: 121 KTLPSADPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLM 180
           +TL S  P   +   +EPLGV+ LITPWNFP++IP WK+APALA GN  VIKPA   P  
Sbjct: 124 ETLQSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLVPGC 183

Query: 181 VAKLVEVLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNK 240
              + E++S+AG P GV NLV+GKG EVG+ IV+  ++ AVSFTGS  VG+ I +     
Sbjct: 184 AWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC--V 241

Query: 241 NRMTRIQLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFK 300
            R  ++QLE+GGKN   V   ADL +A EL  +  F  TGQ CTA+SR+I+ + +Y +F 
Sbjct: 242 ARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRFV 301

Query: 301 QRLLERVKKWRVGPGTED-VDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIP--GK 357
           + ++ER+KK +VG   E  VD+GPVV E Q ++DL YIE GK  GA+L  GG  +    +
Sbjct: 302 EAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGTE 361

Query: 358 GYFLEPTIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIK 417
           GYFL PT+F     +MR+ +EEIFGPV +V + KD DEA+ + N  ++G +AGI  + +K
Sbjct: 362 GYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSLK 421

Query: 418 AINEFVSRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477
             N F    +AG++ +N PT G++   PFGG K S     +E G  A EFY   KT Y G
Sbjct: 422 YANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGP-REQGRYAQEFYTTVKTTYIG 480


Lambda     K      H
   0.316    0.135    0.389 

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: 617
Number of extensions: 25
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: 478
Length of database: 480
Length adjustment: 34
Effective length of query: 444
Effective length of database: 446
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 (21.6 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