GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Herbaspirillum seropedicae SmR1

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate HSERO_RS12030 HSERO_RS12030 phosphate acetyl/butaryl transferase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__HerbieS:HSERO_RS12030
          Length = 484

 Score =  327 bits (839), Expect = 3e-94
 Identities = 168/297 (56%), Positives = 218/297 (73%), Gaps = 1/297 (0%)

Query: 15  LIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLDLGR 74
           L+  AR   PA   V HPCDE SL   ++A   GLI+PILVAP +++  +A  H+LD+  
Sbjct: 187 LLEHARKPGPAPVAVVHPCDELSLAAVLDAHAAGLISPILVAPRSRLLALAESHKLDISA 246

Query: 75  REIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISHVFV 134
             + DVPHSHAAAA+A+ L+  G+ E+LMKGSLHT+E M  V A   GL T+RR+SH ++
Sbjct: 247 FPLEDVPHSHAAAARAIELVMHGKVEMLMKGSLHTEEFMGAVVA-CPGLHTKRRMSHCYL 305

Query: 135 MDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVTAKI 194
           M  P +     ITDAA+NI P L  K DI++NAI+L   IG+  P+VAIL+AVETV  ++
Sbjct: 306 MQTPSYPRPFIITDAAVNIEPGLAEKADIIRNAIELAHVIGVKTPKVAILAAVETVNPRM 365

Query: 195 PSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVPDLE 254
           P+T++AAALCKMA+RGQITG +L+GPLAFDNA+   +AR+KGI S VAG A ILVVPDLE
Sbjct: 366 PATLDAAALCKMADRGQITGAILDGPLAFDNAVSPVSARVKGIRSEVAGQADILVVPDLE 425

Query: 255 AGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRAA 311
           +GN+LAK L ++  A +AGLVLGAR+P++LTSRADS  TRLASCAVA + A   R+A
Sbjct: 426 SGNLLAKQLEYMGGAISAGLVLGARIPLILTSRADSRETRLASCAVARMLAQHYRSA 482


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: 329
Number of extensions: 11
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: 484
Length adjustment: 31
Effective length of query: 285
Effective length of database: 453
Effective search space:   129105
Effective search space used:   129105
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: 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