GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Magnetospirillum magneticum AMB-1

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_000009985.1:WP_043745120.1
          Length = 378

 Score =  252 bits (643), Expect = 1e-71
 Identities = 152/380 (40%), Positives = 210/380 (55%), Gaps = 14/380 (3%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           LT +Q+       D A  E+AP A   DE+ +FPE      A+LG     +    GG+ +
Sbjct: 5   LTPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVGGSAL 64

Query: 64  GVLTLALILEELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYL------RRFAGEST 117
             L  ALI EEL   C STA  +         I   G  E + R+L      R+FA    
Sbjct: 65  SRLDAALIFEELAAACPSTAAYISIHNMAAWMIDSFGDQEQRRRFLPDLCSMRKFA---- 120

Query: 118 LLTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGS 177
              +   TEP AGSD  +++T+A R GD YV+NG K FI+ G  +DV VV   T    G 
Sbjct: 121 ---SYCLTEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTGAP-GP 176

Query: 178 KGISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQT 237
           KGIS  VVE GTPGL +G+ E K+G +    + + FE+  VP  N IGAEG GF   M+ 
Sbjct: 177 KGISCLVVEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKG 236

Query: 238 LSTNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLL 297
           L   R+   A ++G A+  L+ A+ +T  R QFG+ I+     QF +ADMAT +EA+RL+
Sbjct: 237 LDGGRINIGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLM 296

Query: 298 TRKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAK 357
             +AA  LD    +A ++ +MAK MA+D    VT  A+Q+ GG GY+KE  +ER  RD +
Sbjct: 297 IHRAAHSLDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLR 356

Query: 358 LTQIYTGTNQITRMVTGRAL 377
           + QI  G+N+I R++ GRAL
Sbjct: 357 VHQILEGSNEIMRVIIGRAL 376


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: 305
Number of extensions: 9
Number of successful extensions: 3
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: 378
Length adjustment: 30
Effective length of query: 350
Effective length of database: 348
Effective search space:   121800
Effective search space used:   121800
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