GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_041100369.1 SUTH_RS14935 NADP-dependent malic enzyme

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000828635.1:WP_041100369.1
          Length = 760

 Score =  165 bits (417), Expect = 4e-45
 Identities = 106/320 (33%), Positives = 173/320 (54%), Gaps = 11/320 (3%)

Query: 14  ARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA---Y 70
           A+ + + +V  EG+D+R+L AA  + D+ +    ++G P  +++R    GL +       
Sbjct: 436 AKKKPARVVFAEGEDERVLRAAQAVCDEGLARPILIGRPEVVEQRIARYGLRIRPGDHFE 495

Query: 71  LVNPLTDPRLEEFAEQFAELRKSKSVTIDEA-REIMKDISYFGTMMVHNGDADGMVSGAA 129
           LVNP +DPR +E  + + EL   K V I+ A RE+ +  +  G M+V +  AD ++ G  
Sbjct: 496 LVNPDSDPRYKELWQDYYELTCRKGVGIEYAKREMRRRTTLIGAMLVRHNYADALLCGTF 555

Query: 130 NTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSA 189
              +  ++    +I   P      ++ L++L  R    GD  VN +P+AEQ+ E A + A
Sbjct: 556 GKHSLHLRYIADVIGLKPGIENFYAMNLLILPKRTLFIGDTYVNYDPSAEQIAEFARLGA 615

Query: 190 KTAAQFGIDPRVAILSYSTGNSGGGSDVDRAID---ALAEARRLNPELCVDGPLQFDAAV 246
           +   +FG+ PR A+LS+S   + G  D   +I    AL   R + PEL VDG +  D A+
Sbjct: 616 EEVRRFGLAPRAALLSHS---NFGAEDTPTSIKMRRALEILREVAPELEVDGEMHGDTAL 672

Query: 247 DPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRT-GHALAVGPILQGLNKPVNDL 305
              + R+  P+S + GQAN+ I P L+A NI +   + + G  L VGP+L G  +PV+ L
Sbjct: 673 SDDIRRQVFPNSTLKGQANLLIMPTLDAANIAFNLIKTSAGDGLTVGPMLLGAARPVHIL 732

Query: 306 SRGATVPDIVNTVAITAIQA 325
           +  ATV  IVN  A+ +++A
Sbjct: 733 TPTATVRRIVNVTALLSVEA 752


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: 583
Number of extensions: 24
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: 760
Length adjustment: 34
Effective length of query: 295
Effective length of database: 726
Effective search space:   214170
Effective search space used:   214170
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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