GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Azospirillum brasilense Sp245

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate AZOBR_RS17455 AZOBR_RS17455 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__azobra:AZOBR_RS17455
          Length = 387

 Score =  208 bits (529), Expect = 3e-58
 Identities = 128/362 (35%), Positives = 197/362 (54%), Gaps = 19/362 (5%)

Query: 63  IDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDITTFAMVLEEIGKVCASTALMLLAQ 122
           IDE   +P    D     G ++ L+P EYGG+G+ +T  ++++EEI +   ++      Q
Sbjct: 31  IDEERGYPEAFVDALTKAGWMAALIPEEYGGSGLGLTEASVIMEEINRSGGNSGACH-GQ 89

Query: 123 ADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVI 182
              M +++  GS   + +YLP+       + +   TEP  G+D   +KTRA KKGD+YVI
Sbjct: 90  MYNMNTLVRHGSEEQRRRYLPKIAAGELRLQSMGVTEPTTGTDTTRIKTRAEKKGDRYVI 149

Query: 183 NGQKCFITNGSVADILTVWAYTDP----SKGAKGMSTFVVERGTPGLIYGHNEKKMGMRG 238
           NGQK +I+    +D++ + A T P     K ++GMS F+V+      I    +K M ++ 
Sbjct: 150 NGQKVWISRVQHSDLMILLARTTPLDQVRKKSEGMSIFIVD------IKEAMQKGMTVQP 203

Query: 239 CPN------SELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFCASQAVGIAQGALER 292
             N      +ELFF++LE+PAENL+GEEG+GF Y++  L+  RV  A++ +G     +++
Sbjct: 204 IRNMVNHETNELFFDNLEIPAENLIGEEGQGFKYILTGLNAERVLIAAECIGDGYWFIDK 263

Query: 293 AMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLLDAKDKRGPLIGGMA 352
              +TR+R+ FG+PIA    +QF IA+   EVEAA L+  +A  L DA +  G     MA
Sbjct: 264 VCDYTRDRQVFGRPIAQNQGVQFPIAESFIEVEAANLMRFEACRLYDAGEPCGAQ-ANMA 322

Query: 353 KTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY-TGTNQITRMVTGRSLL 411
           K  A+  + +     +Q  GG G+  EY VER  RE +L Q+    TN I   V    L 
Sbjct: 323 KYLAAKASWEAANACLQFHGGFGFASEYDVERKFRETRLYQVAPVSTNLILAYVAEHVLD 382

Query: 412 FP 413
            P
Sbjct: 383 LP 384


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: 344
Number of extensions: 18
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: 387
Length adjustment: 31
Effective length of query: 383
Effective length of database: 356
Effective search space:   136348
Effective search space used:   136348
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