GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Dechlorosoma suillum PS

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Dsui_3032 Dsui_3032 phosphotransacetylase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__PS:Dsui_3032
          Length = 470

 Score =  348 bits (894), Expect = e-100
 Identities = 189/296 (63%), Positives = 220/296 (74%)

Query: 10  SKYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHR 69
           ++Y  L+A A    P    VAHPCD  SL G I AA  GLI P LV PEAKIR+VA E+ 
Sbjct: 167 ARYQALLATAAGLEPIPVAVAHPCDAESLKGPIFAARAGLIEPFLVGPEAKIRSVAEENG 226

Query: 70  LDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRI 129
           LDL    IV+  HSH +AA AV L+R G  E LMKGSLHTDELM EV + A GLRT RRI
Sbjct: 227 LDLTGIRIVNTRHSHESAAMAVTLVRNGDCEALMKGSLHTDELMGEVVSRANGLRTSRRI 286

Query: 130 SHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVET 189
           SHVF MDVP +   + ITDAAINI P LE K DI+QNAIDL+  +G  EP+VAILSAVET
Sbjct: 287 SHVFYMDVPTYPKPIMITDAAINIAPTLEDKVDIIQNAIDLFHILGNPEPKVAILSAVET 346

Query: 190 VTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILV 249
           V  KI ST++AAALCKMA+RGQI GG+L+GPLAFDNA+   AA+ KGI S VAG A ILV
Sbjct: 347 VNPKIQSTLDAAALCKMADRGQIKGGLLDGPLAFDNAVSLVAAKTKGIKSAVAGQADILV 406

Query: 250 VPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYA 305
           VPDLE+GNM+AK L +L +A +AG+VLGA+ PIVLTSRAD+  TR ASCA+AAL A
Sbjct: 407 VPDLESGNMVAKQLEYLANALSAGVVLGAKCPIVLTSRADTAETRTASCAIAALMA 462


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: 9
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: 470
Length adjustment: 30
Effective length of query: 286
Effective length of database: 440
Effective search space:   125840
Effective search space used:   125840
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