GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Rhodobacter viridis JA737

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_003217355.1:WP_110804969.1
          Length = 403

 Score =  258 bits (659), Expect = 2e-73
 Identities = 173/424 (40%), Positives = 238/424 (56%), Gaps = 45/424 (10%)

Query: 1   MRDVFICDAIRTPIG--RFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCAN 58
           M + +I DA RTP G  R  G+L  V +  L+A  L A+ E N  +    V++V +G   
Sbjct: 1   MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERN-GLTGHAVEDVIWGNVT 59

Query: 59  QAGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVE 118
           Q GE    +AR A+LL+GL ESIPG+++NR CASGM+A+  A   + +G     IAGGVE
Sbjct: 60  QVGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVE 119

Query: 119 SMSRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178
            MSR    MG   +  + +  L             MK+ +    +  +AD +A +Y  +R
Sbjct: 120 MMSRV--AMGSDGAAIAVDPSLA------------MKTYFVPQGI--SADVIATEYGFTR 163

Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLK 238
              DA A+ SQ++AA A A   FA+ IVPVR   + G  I+ERDE+LRP TT+E L KLK
Sbjct: 164 EMADALAVESQRRAAEAWAENRFAKSIVPVR--DQNGLIILERDEYLRPGTTMEDLAKLK 221

Query: 239 P--------VNGPDKTVT--------------AGNASGVNDGAAALILASAEAVKKHGLT 276
           P        + G DK                 AGN+SG+ DGAAA+++ S E  + HGL 
Sbjct: 222 PAFKDMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGLK 281

Query: 277 PRARVLGMASGGVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLREL 336
           PRAR+   A  G  P +M  GPVP   K+    G+++SD D+ E+NEAFA+  L  ++  
Sbjct: 282 PRARIRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQAF 341

Query: 337 GVADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALA 396
            V  D  +VN NGGA+ALGHPLG +GA ++ T L +LE+     GLAT+C+  G G A  
Sbjct: 342 DVGQD--KVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAATI 399

Query: 397 IERV 400
           IERV
Sbjct: 400 IERV 403


Lambda     K      H
   0.318    0.134    0.383 

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: 397
Number of extensions: 21
Number of successful extensions: 5
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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 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