GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Rhodobacter viridis JA737

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_003217355.1:WP_110804969.1
          Length = 403

 Score =  256 bits (654), Expect = 8e-73
 Identities = 171/425 (40%), Positives = 229/425 (53%), Gaps = 46/425 (10%)

Query: 1   MNEALIIDAVRTPIG--RYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58
           M EA I DA RTP G  R  G+L  V +  L A  L A+  R+  L   AV+DVI+G   
Sbjct: 1   MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERNG-LTGHAVEDVIWGNVT 59

Query: 59  QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118
           Q GE    +AR A LL+GL  S+PG ++NR C SG++AV  AA  ++ G     +AGGVE
Sbjct: 60  QVGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVE 119

Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
            MSR    MG    A      +   T         + QG        +A+ +A ++  +R
Sbjct: 120 MMSRV--AMGSDGAAIAVDPSLAMKTY-------FVPQGI-------SADVIATEYGFTR 163

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
              DA A+ SQ +AA A A  R AK IV V   + +    I+E DE+ R  TT+E LAKL
Sbjct: 164 EMADALAVESQRRAAEAWAENRFAKSIVPV---RDQNGLIILERDEYLRPGTTMEDLAKL 220

Query: 239 GTPFRQGGSVT----------------------AGNASGVNDGACALLLASSEAAQRHGL 276
              F+  G V                       AGN+SG+ DGA A+L+ S E  + HGL
Sbjct: 221 KPAFKDMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGL 280

Query: 277 KARARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRE 336
           K RAR+   A  G +P IM  GPVP T K+L  +G++++D+D+ E+NEAFAA  L  ++ 
Sbjct: 281 KPRARIRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQA 340

Query: 337 LGLADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIAL 396
             +  D  +VN NGGA+ALGHPLG +GA ++ T L ELE R     L T+CI  G G A 
Sbjct: 341 FDVGQD--KVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAAT 398

Query: 397 IIERI 401
           IIER+
Sbjct: 399 IIERV 403


Lambda     K      H
   0.319    0.134    0.384 

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: 395
Number of extensions: 13
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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