GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Azospirillum brasilense Sp245

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase

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



>FitnessBrowser__azobra:AZOBR_RS28180
          Length = 397

 Score =  254 bits (649), Expect = 3e-72
 Identities = 156/405 (38%), Positives = 233/405 (57%), Gaps = 19/405 (4%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           ++  +I+ A RTP+GR+ G L+++ A  LGA  ++A ++R   L    VD+V+ GC   A
Sbjct: 5   LDPVVIVSAARTPLGRFQGELSALPAHALGAHAVRAALSR-AGLAPERVDEVLLGCVLPA 63

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G+  +  AR AA  AGLP +   TT+N++CGSG+ A   A   +R G A L++AGG+ESM
Sbjct: 64  GQ-GQAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESM 122

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGF-----GIDSMPETAENVAAQFN 175
           S AP+++ K+   +    +        R ++ LM  G      G   M +  E  A  + 
Sbjct: 123 SNAPYLLAKARGGYRIGHD--------RILDHLMLDGLEDAYEGGRPMGDFGEATADLYG 174

Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235
            +RA+QDA+A+ +  +A AAIA+G    EI  V +A  KG  + V  DE+P      E++
Sbjct: 175 FTRAEQDAYAVETLTRARAAIASGAFTAEIAPVTLAV-KGGERTVADDENPL-KVAPEKI 232

Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295
             L   FR+ G++TA ++S   DGA ALLL     A+R GL   A ++G AT   +P   
Sbjct: 233 PALKPAFRRDGTITAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWF 292

Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355
              P+PA RK+L+  G  + D+D+ E+NEAFA   +A  R+LG+  D   +N NGGA AL
Sbjct: 293 TTAPIPAIRKLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRD--ALNVNGGACAL 350

Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           GHP+G +GARL+ T LH L  R  R  + ++CIG G+  A+ +ER
Sbjct: 351 GHPIGATGARLIVTLLHALAARGLRRGVASLCIGGGEATAIAVER 395


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: 425
Number of extensions: 33
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 ( 7.4 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 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