GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Echinicola vietnamensis KMM 6221, DSM 17526

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Echvi_4081 Echvi_4081 Malic enzyme

Query= curated2:Q9ZKU4
         (519 letters)



>FitnessBrowser__Cola:Echvi_4081
          Length = 757

 Score =  207 bits (527), Expect = 1e-57
 Identities = 119/318 (37%), Positives = 188/318 (59%), Gaps = 2/318 (0%)

Query: 204 KAKKQIKKVVLPESEDERILKAAHRLNLMGAVGLILLGDKEAINSQAKNLNLNLENVEII 263
           +AKK  K+VV  E+++ +ILKAA  +N       ILLG++E I    +  +L+L NV II
Sbjct: 437 RAKKHPKRVVFAEADNTKILKAAQLINDERICDPILLGNRETILKLIEEHSLDLSNVPII 496

Query: 264 NPNTSHYR-EEFAKSLYELRKSKGLSEQEAERLALDKTYFATMLVHLGYAHAMVSGVNHT 322
           +P     R E+F   LY  R+ KGL+  EA++L  D+TYF  M+V  G A A++SG+   
Sbjct: 497 DPYEEPERLEKFGNLLYNKRQRKGLTPFEAQKLMRDRTYFGAMMVETGEADALISGLTKD 556

Query: 323 TAETIRPALQIIKTKPGVSLVSSVFLMCLDTQVFVFGDCAIIPNPSPKELAEIATTSAQT 382
             +TI PAL +I  K  V  V+ +++M  D   + F D  +  +P+  ++ EI   +A  
Sbjct: 557 YPKTILPALHVIGVKKDVDRVAGMYIMNSDKGPYFFADTTVNVDPTADQIVEIIGLTADA 616

Query: 383 AKQFNIAPKVALLSYATGNSAQGEMIDKINEALTIVQKLDPQLEIDGPLQFDASIDKGVA 442
            K F++ PKVA+LSY+   SA+G    K   A    ++  P L I+G +Q + +I++ + 
Sbjct: 617 VKFFDLEPKVAVLSYSNFGSAKGNTPTKTALATAKAKEKFPDLIIEGEMQANVAINEAIQ 676

Query: 443 KKKMPNSQVAG-QASVFIFPDLNAGNIAYKAVQRSAKAVAIGPILQGLNKPINDLSRGAL 501
           K+  P S +A  +A+  IFP+L++GNIAYK +     A AIGP+L G+NKP++ L  G+ 
Sbjct: 677 KENYPFSALANKKANTLIFPNLSSGNIAYKLLAEIGNAEAIGPVLLGMNKPVHILQLGSS 736

Query: 502 VEDIVNTVLISAIQAQDY 519
           + +I+N V I+ + AQ +
Sbjct: 737 IREIINMVAIAVVDAQSH 754


Lambda     K      H
   0.316    0.132    0.364 

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: 729
Number of extensions: 36
Number of successful extensions: 3
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: 519
Length of database: 757
Length adjustment: 38
Effective length of query: 481
Effective length of database: 719
Effective search space:   345839
Effective search space used:   345839
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 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