GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas stutzeri RCH2

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__psRCH2:GFF4162
          Length = 701

 Score =  116 bits (290), Expect = 1e-30
 Identities = 86/277 (31%), Positives = 133/277 (48%), Gaps = 45/277 (16%)

Query: 9   QQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEM 68
           Q  + L+T+N P   NAL  A+   L    ++A  D  +    +      F AGAD+ E 
Sbjct: 10  QGEIALITVNNPPV-NALGQAVREGLQKAFQSAEADPQVRAVALVCEGNTFIAGADIKEF 68

Query: 69  AEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLP 128
            +   A +L    P++   ++A NK  +A ++G ALG G E+AL C   +A ++A+ GLP
Sbjct: 69  GKPPQAPSL----PEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYRIARKDAKVGLP 124

Query: 129 EITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLT----- 183
           E+ LG++PGAGGTQRL R  G   A +M++SG+ I+A +A +  +V ++F  DL      
Sbjct: 125 EVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDELFEGDLVEAGLA 184

Query: 184 ---------------------LEYALQLASKMARH-----------SPLALQAAKQALRQ 211
                                LE A   A   A+H           SPL   AA +A   
Sbjct: 185 YVRRMVEEGRTPRRTGEQTQGLEGADNEALIRAKHAEVAKRMPGLFSPLRCIAAVEA--- 241

Query: 212 SQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKR 248
           + ++ L  GL +ER+LF     +  R   + +F  +R
Sbjct: 242 ATKLPLAEGLKRERELFAECLNSPQRGALVHSFFAER 278


Lambda     K      H
   0.318    0.130    0.356 

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: 298
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 701
Length adjustment: 32
Effective length of query: 223
Effective length of database: 669
Effective search space:   149187
Effective search space used:   149187
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 (21.8 bits)
S2: 50 (23.9 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