GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pontibacillus litoralis JSM 072002

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_036834007.1 N784_RS08140 acetyl-CoA C-acyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000775615.1:WP_036834007.1
          Length = 399

 Score =  434 bits (1116), Expect = e-126
 Identities = 230/400 (57%), Positives = 288/400 (72%), Gaps = 4/400 (1%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M E  I D +RTPIGRY GAL  VR DDLAA  ++ LL RNP +    I++V+ G ANQA
Sbjct: 1   MIEVAIVDALRTPIGRYRGALKDVRPDDLAAHVIQGLLERNPNVPIHEIEEVVFGNANQA 60

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           GEDNRNVARMA LLAGLP  V+GTTINRLCGSGLDA+ +AARAI AG+GD+ IAGG ESM
Sbjct: 61  GEDNRNVARMAALLAGLPVEVAGTTINRLCGSGLDAVNYAARAIMAGEGDIFIAGGTESM 120

Query: 121 SRAPFVMGKAASAFSR-QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179
           +RAP+VM K+ ++F R   +++DTTIGWRFVN  +A  +GTDSMPETAENVA+   ISRE
Sbjct: 121 TRAPYVMAKSETSFQRGNPQLYDTTIGWRFVNDKLANMYGTDSMPETAENVAKRYGISRE 180

Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLK 239
            QD FA  SQQ+   A  +GI  +E +PV + ++KG  T I  DEH RP TTL++L  LK
Sbjct: 181 AQDQFAYESQQKAKVAMETGIFEQETIPVTVTDRKGKETVIYEDEHPRPNTTLDKLSQLK 240

Query: 240 APFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299
            P  + G ITAGNASGVNDGA+AL++ S   A   G+ P       A+AG+EP +MGLGP
Sbjct: 241 -PLFSGGTITAGNASGVNDGASALLLMSLNKARELGVKPLVTYHVSASAGLEPNVMGLGP 299

Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359
           + AT++ L R+ L+I  + ++ELNEAFA+Q+L  ++EL L  D   VN NGGAIA GHPL
Sbjct: 300 IYATKKALSRSKLTIKHIGLVELNEAFASQSLQCIKELEL--DTNIVNVNGGAIAFGHPL 357

Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399
           G SGAR+     +E+ RRN +Y L TMC+GVGQGIA I+E
Sbjct: 358 GASGARILTTLIYEMKRRNVQYGLATMCVGVGQGIATIVE 397


Lambda     K      H
   0.319    0.135    0.384 

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: 456
Number of extensions: 9
Number of successful extensions: 4
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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