GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Marinobacter adhaerens HP15

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF2748 HP15_2692 phenylacetate degradation probable enoyl-CoA hydratase paaB

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Marino:GFF2748
          Length = 263

 Score =  151 bits (381), Expect = 1e-41
 Identities = 90/258 (34%), Positives = 137/258 (53%), Gaps = 6/258 (2%)

Query: 4   LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63
           +++   Q V LLTLNRP   N+ N  +  ++   +     D S+ V VITG+ R F AG 
Sbjct: 6   ILLEIDQGVALLTLNRPDNLNSFNVEMHERMREAISTVRKDESVRVLVITGSGRGFCAGQ 65

Query: 64  DLNEMAEK------DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117
           DL++ +        DL A+L +    L   L+    P++ AVNG A GAG  +AL CD+ 
Sbjct: 66  DLSDRSVSPDQEMPDLGASLENYYNPLMRSLRDLPMPVLCAVNGVAAGAGANIALACDIT 125

Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177
           +A  +A F      LG++P +GGT  L R  G + A  M L G+ I+A+QA+  G++   
Sbjct: 126 LAARSANFVQAFCKLGLVPDSGGTWTLPRVAGMARAKGMALLGDKISAEQAENWGMIWRC 185

Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDR 237
             ++  +E  ++LA   A      L   K+AL  S     +  +  ER L  +   TED 
Sbjct: 186 VDNEQLMEETMKLARHFATQPTKGLALIKRALHASASNTFEEQINLERDLQRMAGQTEDY 245

Query: 238 HEGISAFLQKRTPDFKGR 255
            EG++AF++KRTP+FKG+
Sbjct: 246 REGVAAFMEKRTPNFKGK 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: 122
Number of extensions: 6
Number of successful extensions: 2
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