GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Methylocapsa aurea KYG

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_036258927.1 DL86_RS05200 acetyl-CoA C-acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000746085.1:WP_036258927.1
          Length = 391

 Score =  334 bits (856), Expect = 3e-96
 Identities = 185/401 (46%), Positives = 258/401 (64%), Gaps = 11/401 (2%)

Query: 1   MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60
           MSRE+ I  A RT +G F G+ AA  A +L A  +KA ++R  ++D + +DEV LG    
Sbjct: 1   MSREIVIVSAARTAVGSFNGAFAATPAHELGAAAIKAALDR-AKIDAADVDEVILGQVLT 59

Query: 61  AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120
           AG+  +N AR A + AG+P       LN++C SG+ AV  A + IA+G+AE+V+AGG ES
Sbjct: 60  AGQ-GQNPARQAAIKAGIPQEKTAFGLNQVCGSGLRAVALAAQQIATGDAEIVVAGGQES 118

Query: 121 MSRAPYVMGKADSAFGR-GQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSR 179
           MS++ +       A+ R G K+ D       +   +   +    M +TA+NVA  ++++R
Sbjct: 119 MSQSQH------GAYLRSGVKMGDLKFVDTMLRDGLTDVFNGYHMGQTAENVAAKWQITR 172

Query: 180 ADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLK 239
            +QD FAL SQ  A  AQ  G F EEI P  +  +KG+ V+DADE++R   TL+ LAKLK
Sbjct: 173 DEQDRFALASQNKAEAAQKEGRFKEEIAPFTVTSRKGDVVIDADEYIRLGATLDGLAKLK 232

Query: 240 PVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299
           P    D TVTAGNASG+NDG  AL+L SA+     GL   A++   ASAGV P +MG GP
Sbjct: 233 PAFAKDGTVTAGNASGINDGGAALVLMSAKDAAARGLTPLARIASWASAGVDPALMGSGP 292

Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359
           +PA RK LE+    V D D++E NEAFAAQ LAV +++G   D A VN NGGAIA+GHP+
Sbjct: 293 IPASRKALEKAGWKVKDLDLVEANEAFAAQALAVNKDMGW--DPAIVNVNGGAIAIGHPI 350

Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           GASGAR+++T +H++++ G ++GL T+C+G G G+AL VER
Sbjct: 351 GASGARVLITLLHEMQRRGAKKGLATLCIGGGMGIALTVER 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: 425
Number of extensions: 22
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: 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