GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Sinorhizobium meliloti 1021

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  162 bits (409), Expect = 8e-45
 Identities = 99/251 (39%), Positives = 146/251 (58%), Gaps = 7/251 (2%)

Query: 12  VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNE--- 67
           + LLTLNRP   NALN  L+ +L+  L+    D ++   ++TG   R F+AG D++E   
Sbjct: 13  IALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFSAGGDIHEFSG 72

Query: 68  -MAEKDLAATLNDTR--PQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENAR 124
            +A+   AAT +  R   QL  RL+AF KP+IAAVNG A G GCE+     + +A E AR
Sbjct: 73  SVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAVHLAIASERAR 132

Query: 125 FGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTL 184
           F  PEI L + P  GGTQRL R  G+  A +++L+G++ + Q+A   GLV+ V P +  +
Sbjct: 133 FAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLVNAVVPHEQLI 192

Query: 185 EYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAF 244
             A  LA +  RHSPLA  A   A+ +   +A+  GL  E + F  +  + D  EG++A+
Sbjct: 193 ASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARMVPSHDLKEGLAAW 252

Query: 245 LQKRTPDFKGR 255
            ++R P + GR
Sbjct: 253 KERREPRYAGR 263


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: 120
Number of extensions: 4
Number of successful extensions: 1
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: 255
Length of database: 263
Length adjustment: 24
Effective length of query: 231
Effective length of database: 239
Effective search space:    55209
Effective search space used:    55209
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: 47 (22.7 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