GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Burkholderia phytofirmans PsJN

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate BPHYT_RS27695 BPHYT_RS27695 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__BFirm:BPHYT_RS27695
          Length = 467

 Score =  317 bits (812), Expect = 4e-91
 Identities = 173/315 (54%), Positives = 214/315 (67%), Gaps = 9/315 (2%)

Query: 5   WPAQPS---------KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILV 55
           WP  PS         +Y+  I  AR      T + HPC   ++  AIEA + GL+ P+L+
Sbjct: 148 WPCAPSTEVTLRRHDRYEAFIRQARTRPALRTAIVHPCSAEAIVAAIEARDEGLLEPVLI 207

Query: 56  APEAKIRNVAAEHRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHE 115
            P+A+IR  A    +DL    I  V HSHAAAA+AV +   G+   LMKGSLHTDEL+  
Sbjct: 208 GPDARIRAAAEAANVDLAGVPIEAVEHSHAAAARAVEMGAAGQVAALMKGSLHTDELLGA 267

Query: 116 VAASATGLRTQRRISHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIG 175
           V A  +GLRT RRISHV+ MDVP ++  L +TDA +NI P L+ KRDI QNAIDL   +G
Sbjct: 268 VVARNSGLRTARRISHVYAMDVPAYSKPLVVTDAVVNIAPSLDHKRDICQNAIDLLHVLG 327

Query: 176 LGEPRVAILSAVETVTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIK 235
               RVA L A+ETV +++P+T++AAAL  MA RGQITG +++GPLAFDNAI   AA+ K
Sbjct: 328 AELARVAALGAIETVNSRMPATLDAAALTVMAARGQITGALVDGPLAFDNAISLAAAKTK 387

Query: 236 GINSPVAGHAQILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRL 295
            I+SPVAG A IL+VPDLEAGN+LAK L +   ADAAGLVLGARVPI+LTSRADSVR RL
Sbjct: 388 QIDSPVAGQADILLVPDLEAGNILAKQLMYFAGADAAGLVLGARVPIILTSRADSVRVRL 447

Query: 296 ASCAVAALYAARRRA 310
           AS A+A L A R  A
Sbjct: 448 ASAALAKLVAERTLA 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: 358
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 316
Length of database: 467
Length adjustment: 30
Effective length of query: 286
Effective length of database: 437
Effective search space:   124982
Effective search space used:   124982
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