GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Sinorhizobium meliloti 1021

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate SMc01639 SMc01639 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Smeli:SMc01639
          Length = 386

 Score =  194 bits (492), Expect = 5e-54
 Identities = 136/386 (35%), Positives = 199/386 (51%), Gaps = 16/386 (4%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFP-----EYARDLFAKLGLLNPLLPAAY 58
           LTEEQ++ +D VR     EI P   E++   + P     E AR    +LG      P   
Sbjct: 5   LTEEQQMIVDTVRTFVETEIYPHENEVERTGVVPRELGLEIARKC-KELGFFACNFPEEV 63

Query: 59  GGTEMGVLTLALILEELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTL 118
           GG  +  LT  L+  ELGR      +    +  G+L   +    + +ERYL   A     
Sbjct: 64  GGAGLDHLTFTLVERELGRGSMGLTVFF-GRPSGILMACN---EDQRERYLLP-AVRGDK 118

Query: 119 LTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSK 178
             ALA TEP AGSD+  MK  A   GD +++NG K FI++  +AD ++V+  T  E+  +
Sbjct: 119 FDALAMTEPDAGSDVRGMKCFARPDGDDWIVNGTKHFISHADIADFVIVFIATGEEQTPR 178

Query: 179 G----ISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANL 234
           G    I+ F+V++GTPG       + +  RG  N  L F++  +P+  I+G    GF   
Sbjct: 179 GPKKKITCFLVDRGTPGFEIREGYNSVSHRGYKNCILTFDDCRLPSAQILGEVHKGFDIA 238

Query: 235 MQTLSTNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEAS 294
              L   R+  AA +VG A+ A D A+ +  +R QFGKPI+    V F +ADM T ++A+
Sbjct: 239 NDWLYATRLTVAATSVGRARRAFDYALSYAAERKQFGKPISANQGVSFKLADMITEIDAA 298

Query: 295 RLLTRKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMR 354
            LLT  AA  LD G        S AK  A++   RVT +A+Q+ GG G M +  + R  R
Sbjct: 299 DLLTLSAAWRLDQGLPSNREIAS-AKVFATEMLARVTDEAIQIYGGMGLMDDLPLARFWR 357

Query: 355 DAKLTQIYTGTNQITRMVTGRALLFP 380
           DA++ +I+ GT++I R +  R LL P
Sbjct: 358 DARVERIWDGTSEIQRHIISRDLLRP 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: 335
Number of extensions: 17
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