GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Paraburkholderia bryophila 376MFSha3.1

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate H281DRAFT_01410 H281DRAFT_01410 phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__Burk376:H281DRAFT_01410
          Length = 311

 Score =  379 bits (972), Expect = e-110
 Identities = 197/299 (65%), Positives = 235/299 (78%)

Query: 11  KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70
           KY RLIA  +++ P  T VAHPCD  SL GA+EAA+MGLI P+LV P  +I  VA E  L
Sbjct: 7   KYQRLIAFCQSQPPLTTAVAHPCDRASLEGAVEAAQMGLIAPLLVGPRERISAVAEECGL 66

Query: 71  DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130
            +    ++DVPHSHAAAAKAV L+REG+ E +MKGSLHTDELM  V     GLRT+RR+S
Sbjct: 67  QIAGYPLIDVPHSHAAAAKAVELVREGKAEAIMKGSLHTDELMAAVVHREGGLRTERRVS 126

Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190
           H FVMDVPGH + L ITDAAINI P L  K DI+QNAIDL  A+ + E RVAILSA+E V
Sbjct: 127 HCFVMDVPGHANALIITDAAINIAPTLAEKTDILQNAIDLGHALRVDEVRVAILSAMEIV 186

Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250
             K+PSTIEAAALCKM +R QITG +++GPLA DNAID EAAR+K I+SPVAG A +L+V
Sbjct: 187 NPKVPSTIEAAALCKMVDRHQITGALVDGPLALDNAIDLEAARMKKIDSPVAGRANVLMV 246

Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRR 309
           P+LEAGNMLAK+L+FL  ADAAG+VLGARVPI+LTSRADS+ TRLASCAVA+L A++ R
Sbjct: 247 PNLEAGNMLAKSLSFLAGADAAGIVLGARVPIILTSRADSIITRLASCAVASLVASKGR 305


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: 287
Number of extensions: 6
Number of successful extensions: 1
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: 311
Length adjustment: 27
Effective length of query: 289
Effective length of database: 284
Effective search space:    82076
Effective search space used:    82076
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.

Links

Downloads

Related tools

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