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_3725 PP_3725 putative Acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Putida:PP_3725
          Length = 386

 Score =  210 bits (535), Expect = 5e-59
 Identities = 144/386 (37%), Positives = 210/386 (54%), Gaps = 16/386 (4%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEK-SLFPEYARDLFAKL---GLLNPLLPAAYG 59
           LT+EQ++ ++ VR    +E+ P    +D   ++ PE A  +  K    G     +P   G
Sbjct: 5   LTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMPEEVG 64

Query: 60  GTEMGVLTLALILEELGRVCASTAL-LLIAQTDGMLPIIHGGSPELKERYLRRFAGESTL 118
           G  +  L+ ALI  EL +V  S AL + +A+   +L        ++ +  L    GE   
Sbjct: 65  GGGLDYLSQALIERELSKV--SWALHVFVARPSKILMACK--DEQINDYLLPCVQGEK-- 118

Query: 119 LTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDP--EKG 176
           +   A TEP AGSD  A+KTRAVRQGD +VING K FI++   AD  +V+A TD     G
Sbjct: 119 VDCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYEHNG 178

Query: 177 SK--GISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANL 234
            K   ++A +V++GTPG+   R    +  RG    ELFF++  VPA  ++G  G G+   
Sbjct: 179 RKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGWEVA 238

Query: 235 MQTLSTNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEAS 294
              L+  RV  AA  VG AQ ALD++++   DR QFG+ I     V F +ADMAT + A+
Sbjct: 239 NAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQIRAA 298

Query: 295 RLLTRKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMR 354
            +LT   A  +D G+      G MAK  AS+   +V  +AVQ+ GG G M E  VER+ R
Sbjct: 299 EMLTLHTAWKMDQGNMTDGEAG-MAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERIWR 357

Query: 355 DAKLTQIYTGTNQITRMVTGRALLFP 380
           +A++ +I+ GT++I R +  R LL P
Sbjct: 358 NARIERIWEGTSEIQRHIIARELLRP 383


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: 284
Number of extensions: 14
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: 380
Length of database: 386
Length adjustment: 30
Effective length of query: 350
Effective length of database: 356
Effective search space:   124600
Effective search space used:   124600
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.

Links

Downloads

Related tools

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