GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Acidovorax sp. GW101-3H11

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate Ac3H11_1079 NADP-dependent malic enzyme (EC 1.1.1.40)

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1079
          Length = 768

 Score =  142 bits (357), Expect = 4e-38
 Identities = 99/315 (31%), Positives = 154/315 (48%), Gaps = 7/315 (2%)

Query: 21  IVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTAYLV---NPLTD 77
           +   +G+D+R L AA   +D  I    ++G P  I  R  + GL +     V   NP  D
Sbjct: 454 VAYADGEDERALRAAQMAIDDKIATPILIGRPAVIAARIAKAGLRMQLGKDVEVCNPEDD 513

Query: 78  PRLEEFAEQFAELRKSKSVTIDEARE-IMKDISYFGTMMVHNGDADGMVSGAANTTAHTI 136
           PR  ++ E + +L K    T + A+  + +  +   ++MV  GDAD M+ G   T    +
Sbjct: 514 PRFRQYWEHYHQLMKRNGATPEVAKAAVRRSNTIIASLMVKLGDADAMICGLVGTYETHL 573

Query: 137 KPSFQIIKTVPEASVVSSI-FLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSAKTAAQF 195
           +    II     A   +++  LM  RG L+   D  VN +PTA+QL +IA +S +   +F
Sbjct: 574 ERIHSIIGRQEGARDYAALNALMTNRGTLF-IADTYVNEDPTAQQLADIAWMSVQEVQRF 632

Query: 196 GIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAAVDPGVARKKM 255
           G+ P+VA LS+S+  S   +   +  +A       +PE+  DG L  DAA++P +    M
Sbjct: 633 GLPPKVAFLSHSSYGSSKRASARKMREARDLFVAAHPEIECDGELHGDAALEPNIRNAYM 692

Query: 256 PDSDVAGQANVFIFPDLEAGNIGYKTAQ-RTGHALAVGPILQGLNKPVNDLSRGATVPDI 314
            DS +   AN+ I P+L+A NI Y   +  T   + VGPIL G       L+  ATV  +
Sbjct: 693 ADSTLTDSANLLICPNLDAANILYNVLKTTTSGGVTVGPILMGGAATAYILTPAATVRRV 752

Query: 315 VNTVAITAIQAGGRS 329
            N  A+    A  R+
Sbjct: 753 FNMTALAVASAAARA 767


Lambda     K      H
   0.318    0.134    0.386 

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: 539
Number of extensions: 29
Number of successful extensions: 5
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: 329
Length of database: 768
Length adjustment: 34
Effective length of query: 295
Effective length of database: 734
Effective search space:   216530
Effective search space used:   216530
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 (21.7 bits)
S2: 52 (24.6 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