GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Marinobacter adhaerens HP15

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Marino:GFF2
          Length = 389

 Score =  246 bits (627), Expect = 1e-69
 Identities = 142/377 (37%), Positives = 212/377 (56%), Gaps = 6/377 (1%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L E   +L E +   A  EIAPRA EID N+ FP+       D+GLL   V  EYGG+ M
Sbjct: 12  LGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDM 71

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSII-LDGSPALKEKYLPRF--GEKSTLMT 153
                 + +EEI +  AS  L   A ++  ++ I  +G+   K+KYLP+   GE    + 
Sbjct: 72  GYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEH---IG 128

Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213
           A A +EP AGSD+++MK  A  +GD Y++NG K +ITNG  A+   ++A TD S G++G+
Sbjct: 129 ALAMSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGV 188

Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273
           + F+VER  PG        K+GMRG    EL F+D +VP EN++G  G G   LM  L  
Sbjct: 189 TAFIVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDY 248

Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333
            R+  +   +GI Q A++  + + RER+QFG+ I     +Q  +ADM T +  A+  V  
Sbjct: 249 ERLVLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYM 308

Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393
                D   +        A  ++++ A K+  DA+Q++GG+GY+ EY   R++R+AKL +
Sbjct: 309 VAMSADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAKLYE 368

Query: 394 IYTGTNQITRMVTGRSL 410
           I  GT++I RM+ GR L
Sbjct: 369 IGAGTSEIRRMLIGREL 385


Lambda     K      H
   0.318    0.133    0.375 

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: 379
Number of extensions: 14
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: 414
Length of database: 389
Length adjustment: 31
Effective length of query: 383
Effective length of database: 358
Effective search space:   137114
Effective search space used:   137114
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 (21.7 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