GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Rhodobacter viridis JA737

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_110804635.1 C8J30_RS05090 acetyl-CoA C-acyltransferase family protein

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_003217355.1:WP_110804635.1
          Length = 391

 Score =  240 bits (613), Expect = 4e-68
 Identities = 158/399 (39%), Positives = 216/399 (54%), Gaps = 25/399 (6%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MT  VI+S ART IG A+ G+L       L   A   A++R+GI P+++  VVMG  +  
Sbjct: 1   MTGIVILSGARTAIG-AFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNT 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
                 ++R A ++AG+PV T    ++R C SG+QAI  AA++++    + A+ GG + +
Sbjct: 60  EPRDMYVSRVAAIQAGIPVETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVM 119

Query: 121 SLVQ--------NDKMNTFHAVDPALEAIK---GDVYMAMLDTAETVAKRYGISRERQDE 169
           S             KM     +D  + A+    G  +M +  TAE VA    ISRE QD 
Sbjct: 120 SRAPYILPAARFGQKMGDASVIDMMVGALSCPFGTGHMGV--TAENVATECAISREDQDT 177

Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229
           ++LESQ R AAA   G F DEI P+      +    G V F       DE P+  TT + 
Sbjct: 178 FALESQTRAAAAIAAGAFKDEIVPVE-----IASRKGTVIF-----DTDEHPKA-TTLDK 226

Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289
           LA LK    +G ++TAGNAS ++DGA A VI  +  A A GLKPL   RG    G  P+ 
Sbjct: 227 LAALKPAFLKGGSVTAGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEV 286

Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349
           MG+GP+ AV  L ++ GL V D  + E NEAFA Q L     L +DP K+N NGGAI++G
Sbjct: 287 MGLGPIPAVRLLCEKTGLKVSDFDVIESNEAFAAQALAVSRALDLDPTKVNPNGGAIALG 346

Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           HP G +GA L    L   RR   +  ++TMC+GGG G A
Sbjct: 347 HPVGATGAILTVKTLYHLRRTGGRLGLITMCIGGGQGIA 385


Lambda     K      H
   0.316    0.134    0.378 

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: 454
Number of extensions: 17
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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