GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Methylocapsa aurea KYG

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_036260250.1 DL86_RS07955 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000746085.1:WP_036260250.1
          Length = 402

 Score =  258 bits (660), Expect = 2e-73
 Identities = 173/424 (40%), Positives = 227/424 (53%), Gaps = 45/424 (10%)

Query: 1   MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58
           M EAFI D +RTP GR    GAL  V +  LA   LR +  R   LD   +DDVILGC +
Sbjct: 1   MAEAFIYDHVRTPRGRGKSDGALHEVSSLGLATTVLRAIKDRGD-LDTALVDDVILGCVD 59

Query: 59  QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118
             GE   ++AR A L A     V G  INR C SGLDA+ FAA  + AG  +L I GGVE
Sbjct: 60  PVGEAGGDIARAAALTADYGDHVPGVQINRFCASGLDAVNFAAAQVMAGQHELTIGGGVE 119

Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178
           SMSR    +G +  A+               V+P +A +        +A+ +A     SR
Sbjct: 120 SMSRVG--LGASGGAWP--------------VDPAIAIKSYFMPQGVSADLIATKYGFSR 163

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           +D D++A+ SQQR A A S G   + + PV  ++  G VT +  DEH+RP T ++ L  L
Sbjct: 164 DDVDAYAVLSQQRAAAAWSKGYFTQSLAPV--RDVNG-VTLLDRDEHMRPSTDMQSLAAL 220

Query: 239 KAPFRANG---------------------VITAGNASGVNDGAAALIIASEQMAAAQGLT 277
           K  F   G                     V  AGN+SG+ DGA A+++ S +   +    
Sbjct: 221 KPAFAMMGEQGGFDAVAIDAHPDIERVVHVHHAGNSSGIVDGAGAVLVGSAEAGRSIEKK 280

Query: 278 PRARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLREL 337
           PRA+I A A  G EP +M  GPV  T++VL RAG++I D+D+ E+NEAFA+  L  L+  
Sbjct: 281 PRAKIRAFANIGSEPAMMLTGPVDVTKKVLARAGMNIGDIDLFEVNEAFASVVLRYLQAF 340

Query: 338 GLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMI 397
            L  D   +N NGGAIA+GHPLG +GA L   A  EL R     AL T+CIG G G A I
Sbjct: 341 DL--DVEKLNVNGGAIAMGHPLGATGAMLLGTALDELERSGKTTALITLCIGAGMGTATI 398

Query: 398 LERV 401
           +ERV
Sbjct: 399 IERV 402


Lambda     K      H
   0.319    0.135    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: 440
Number of extensions: 23
Number of successful extensions: 6
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: 402
Length adjustment: 31
Effective length of query: 370
Effective length of database: 371
Effective search space:   137270
Effective search space used:   137270
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 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