GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Methylocystis bryophila S285

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_002117405.1:WP_085770214.1
          Length = 391

 Score =  320 bits (819), Expect = 6e-92
 Identities = 178/400 (44%), Positives = 259/400 (64%), Gaps = 9/400 (2%)

Query: 1   MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60
           M+ ++ I  A RT +G F G+   V A +L A  VK+ +ER  +V  S++ EV LG    
Sbjct: 1   MTTDIVIVSAARTAVGSFNGAFGGVPAHELGAAAVKSALER-AKVAPSEVCEVILGQVLG 59

Query: 61  AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120
           A +  +N AR A + AG+PDS     +N++C SG+ AV  A + I +G+A++V+AGG ES
Sbjct: 60  AAQ-GQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQES 118

Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180
           MS + +      +    G K+   +     I   +   +    M  TA+NVA  +++SRA
Sbjct: 119 MSLSTHA-----AHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRA 173

Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240
           +QDAFA+ SQ  A  AQ AG F +EI+P  I  +KG+ VVD+DE+++   TLE+++KL+P
Sbjct: 174 EQDAFAVASQNKAEAAQKAGKFKDEILPYTISTRKGDVVVDSDEYVKHGVTLESVSKLRP 233

Query: 241 VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300
               D TVTA NASG+NDG+ AL++ SA   KK GL+  A++   A+AGV P +MG GP+
Sbjct: 234 AFTKDGTVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPI 293

Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360
           PA RK LE+    V+D +++E NEAFAAQ +AV ++LG   D A VN NGGAIA+GHP+G
Sbjct: 294 PATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLGW--DPAIVNVNGGAIAIGHPIG 351

Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           ASGAR++ T +++L++ GG +GL T+C+G G G+ALAVER
Sbjct: 352 ASGARILTTLLYELKRRGGGKGLATLCIGGGMGIALAVER 391


Lambda     K      H
   0.317    0.134    0.379 

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: 412
Number of extensions: 12
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 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