GapMind for catabolism of small carbon sources

 

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

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_171817353.1 SUTH_RS10365 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>NCBI__GCF_000828635.1:WP_171817353.1
          Length = 472

 Score =  345 bits (884), Expect = 2e-99
 Identities = 184/300 (61%), Positives = 225/300 (75%)

Query: 10  SKYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHR 69
           ++++ L+   +   P    VAHPCD  SL GA+ A + GLI P LV PE KIR +A  ++
Sbjct: 170 ARFEHLLEITKGLTPISMAVAHPCDTESLKGALLARDRGLIIPTLVGPEEKIRQLAEANQ 229

Query: 70  LDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRI 129
           LDL    +++V HSHAAA  AV+L REG+ E LMKGSLHTDELM EV   ATGLRT RRI
Sbjct: 230 LDLYGCTVINVAHSHAAAEIAVSLAREGQVEALMKGSLHTDELMSEVIDKATGLRTARRI 289

Query: 130 SHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVET 189
           SHVF+MDVP +   LFITDAA+N+ PDLEAK DIVQNAIDL   + + +P+VAIL+AVET
Sbjct: 290 SHVFLMDVPTYPRLLFITDAAVNVAPDLEAKVDIVQNAIDLAHMLKIADPKVAILAAVET 349

Query: 190 VTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILV 249
           V  K+ +T++AAALCKMA+RGQITGG+L+GPLAFDNAI   AAR KGI S VAG A IL+
Sbjct: 350 VNLKMQATLDAAALCKMADRGQITGGLLDGPLAFDNAISVVAARTKGIKSAVAGQADILL 409

Query: 250 VPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRR 309
           VPD+E+GNMLAK L +L  A  +G+VLGA+VPIVLTSRADS  TR AS AVA + A  +R
Sbjct: 410 VPDIESGNMLAKQLEYLADALTSGIVLGAKVPIVLTSRADSAETRTASTAVAMVMAHAKR 469


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: 317
Number of extensions: 12
Number of successful extensions: 2
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: 472
Length adjustment: 30
Effective length of query: 286
Effective length of database: 442
Effective search space:   126412
Effective search space used:   126412
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 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