GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Methylocystis bryophila S285

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_085772269.1 B1812_RS14765 acyl-CoA dehydrogenase family protein

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_002117405.1:WP_085772269.1
          Length = 557

 Score =  200 bits (509), Expect = 7e-56
 Identities = 133/376 (35%), Positives = 202/376 (53%), Gaps = 15/376 (3%)

Query: 15  VRDVATREIAPRALELDEKSLF-PEYARDLFAKLGLLNPLLPAAYGGTEMGVLTLALILE 73
           +R  A+  + P A E   K+ + P       A+LG+    +P  +GG+ MG + + ++ E
Sbjct: 183 MRKFASDNVTPFAQEWHAKNEYIPLEVISGLAELGVFGLTIPEEFGGSGMGKIAMCVVSE 242

Query: 74  ELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALAATEPAAGSDL 133
           EL R       L          I+ GG+   KE+YL + A    L TA+  TEP  GSDL
Sbjct: 243 ELSRAYIGVGSLGTRSEIAGELILVGGTKAQKEKYLPKIAAGEILPTAVF-TEPNNGSDL 301

Query: 134 LAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPE-KGSKGISAFVVEK--GTP 190
             ++TRAVR+GD Y + G K +IT+   ADV+ +   T+PE KG KG+S  + EK  GT 
Sbjct: 302 AGLRTRAVREGDVYKVTGNKTWITHPVRADVMTLLVRTNPEEKGYKGLSMLLAEKPRGTD 361

Query: 191 -------GLVYGRNESKMGMRGSINSELFFENMEVPAENIIGA-EGTGFANLMQTLSTNR 242
                  G+  G  E  +G RG    E+ F+  E PAEN++G  EG GF  LM+T  + R
Sbjct: 362 ENPFPAKGMTGGEIEV-LGYRGMKEFEIGFDGFETPAENLLGGVEGNGFKQLMETFESAR 420

Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302
           +  AA+A+G+AQ ALD+ +R+ ++R+QFGKP+     +   +  MA  +  +R +T  +A
Sbjct: 421 IQTAARALGVAQCALDLGLRYAKERIQFGKPLFSFPRIFDKIVAMAVEIHVARQITYFSA 480

Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362
               DG K+  L   MAK + +  A     +A+Q+ GG+G+  E  V R++ DA++  I+
Sbjct: 481 R-QKDGGKRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYPVSRVLCDARILNIF 539

Query: 363 TGTNQITRMVTGRALL 378
            G  +I   V  R LL
Sbjct: 540 EGAAEIQAQVIARRLL 555


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: 418
Number of extensions: 23
Number of successful extensions: 8
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: 557
Length adjustment: 33
Effective length of query: 347
Effective length of database: 524
Effective search space:   181828
Effective search space used:   181828
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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