GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Azospirillum brasilense Sp245

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate AZOBR_RS32455 AZOBR_RS32455 phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__azobra:AZOBR_RS32455
          Length = 332

 Score =  227 bits (578), Expect = 3e-64
 Identities = 135/302 (44%), Positives = 176/302 (58%), Gaps = 1/302 (0%)

Query: 14  RLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLDLG 73
           RL+A + A  P  T V       +L  A  A  +GLI P+LV     I + A      L 
Sbjct: 15  RLMARSAALEPVPTAVVAAGSPVALESARRATALGLIEPVLVGDPTAIADSARRIGWTLH 74

Query: 74  RREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISHVF 133
              +V      AAA  AVAL R G    LMKG +HTD LM        GLRT RR +H F
Sbjct: 75  GACVVPARDDAAAARIAVALARSGDVGALMKGHIHTDTLMLAALHPKNGLRTGRRFTHAF 134

Query: 134 VMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVTAK 193
            M +PG    L ITDAAIN+ P L  + DI++NA++LW  +G  +PRVA+LS  E VT +
Sbjct: 135 HMTLPGSGRELVITDAAINVAPSLNTRLDIIRNAVELWRLVGGSDPRVALLSCTEEVTER 194

Query: 194 IPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVPDL 253
           +PS+++A  L ++ ++ ++ G  + GPLA D A+  EAARIK +  P AG A ILVVP++
Sbjct: 195 VPSSMDADRLTRLCQQ-EVPGATVFGPLALDLAVSAEAARIKNLTHPCAGAADILVVPNI 253

Query: 254 EAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRAAQV 313
           E GN L K L     A AAG+VLGA VPIVLTSRAD    R+A+ A+A + A RRR+A  
Sbjct: 254 ETGNALFKALVHFLDAVAAGVVLGAAVPIVLTSRADPPAARIAAAAIAQIVAGRRRSATP 313

Query: 314 AA 315
            A
Sbjct: 314 GA 315


Lambda     K      H
   0.320    0.133    0.376 

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: 256
Number of extensions: 6
Number of successful extensions: 2
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: 316
Length of database: 332
Length adjustment: 28
Effective length of query: 288
Effective length of database: 304
Effective search space:    87552
Effective search space used:    87552
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 (21.9 bits)
S2: 48 (23.1 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