GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Azospirillum brasilense Sp245

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__azobra:AZOBR_RS28180
          Length = 397

 Score =  267 bits (683), Expect = 4e-76
 Identities = 162/396 (40%), Positives = 227/396 (57%), Gaps = 8/396 (2%)

Query: 5   VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64
           V I  A RTP+GRF G L+A+ A  L A  V+A + R       ++DEV LGC   AG+ 
Sbjct: 8   VVIVSAARTPLGRFQGELSALPAHALGAHAVRAALSRAGLAP-ERVDEVLLGCVLPAGQ- 65

Query: 65  NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124
            +  AR A   AGLPD+    T+N++C SGM A   A   I +G A+LV+AGG+ESMS A
Sbjct: 66  GQAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESMSNA 125

Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184
           PY++ KA   +  G    D  +    ++ L  A  G   M +  +  AD Y  +RA+QDA
Sbjct: 126 PYLLAKARGGYRIGH---DRILDHLMLDGLEDAYEGGRPMGDFGEATADLYGFTRAEQDA 182

Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244
           +A+ +   A  A A+G F  EI PV +  K GE  V AD+        E +  LKP    
Sbjct: 183 YAVETLTRARAAIASGAFTAEIAPVTLAVKGGERTV-ADDENPLKVAPEKIPALKPAFRR 241

Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304
           D T+TA ++S   DG+ AL+L      ++ GL   A +LG A+    P      P+PA+R
Sbjct: 242 DGTITAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWFTTAPIPAIR 301

Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364
           KLL+R+   + D D+ E+NEAFA   +A  R+LGI  D   +N NGGA ALGHP+GA+GA
Sbjct: 302 KLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRD--ALNVNGGACALGHPIGATGA 359

Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           RL++T +H L   G +RG+ ++C+G G+  A+AVER
Sbjct: 360 RLIVTLLHALAARGLRRGVASLCIGGGEATAIAVER 395


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: 428
Number of extensions: 22
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: 397
Length adjustment: 31
Effective length of query: 370
Effective length of database: 366
Effective search space:   135420
Effective search space used:   135420
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 Sep 17 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