GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Pseudomonas putida KT2440

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PP_2216 PP_2216 short-chain acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Putida:PP_2216
          Length = 375

 Score =  271 bits (694), Expect = 2e-77
 Identities = 152/375 (40%), Positives = 226/375 (60%), Gaps = 3/375 (0%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           + +EQ+   D VR  A   + P A + D+   FP+ A D  A+LGL   L+P  +GG++ 
Sbjct: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62

Query: 64  GVLTLALILEELGRVC-ASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTAL 122
           G +  A+ LEE+     A + ++ +  + G +PI+  G+ + KE++L   A    +L A 
Sbjct: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLA-TGAMLGAF 121

Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182
           A TEP AGSD  ++KTRA  +GD YV+NG K FIT+G  A V++V+A TDPE G +GISA
Sbjct: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181

Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242
           F+V   +PG    R E K+G   S   ++ F+N++VP  N +GAEG G+   +  L   R
Sbjct: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241

Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302
           +  A+QAVG+A+ A ++A  +  +R  FGKP+     V F +ADMAT +  +R +   AA
Sbjct: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301

Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362
            L D G + A++  SMAK  AS+ A +V +DA+Q LGG GY+ +  +ER+ RD ++ QIY
Sbjct: 302 ALRDAG-RPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIY 360

Query: 363 TGTNQITRMVTGRAL 377
            GT+ I RMV  R L
Sbjct: 361 EGTSDIQRMVIARNL 375


Lambda     K      H
   0.319    0.134    0.371 

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: 308
Number of extensions: 12
Number of successful extensions: 4
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: 380
Length of database: 375
Length adjustment: 30
Effective length of query: 350
Effective length of database: 345
Effective search space:   120750
Effective search space used:   120750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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