GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Rhodanobacter denitrificans 2APBS1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_007508344.1 R2APBS1_RS08710 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000230695.2:WP_007508344.1
          Length = 401

 Score =  301 bits (771), Expect = 2e-86
 Identities = 189/415 (45%), Positives = 245/415 (59%), Gaps = 32/415 (7%)

Query: 1   MNEALIIDAVRTPIGRYA-GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQ 59
           + EA I+ A RTP+G+   G   + R DD+ A  ++A++A+ P +D   + DVI GCA  
Sbjct: 5   VQEAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDPHQIGDVIIGCAMP 64

Query: 60  AGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVES 119
             E   NVAR+  LLAGLP +VPG T+NR C SGL +V  AA  +R G   LMLAGG ES
Sbjct: 65  EAEQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGLQSVAMAADRIRLGLDDLMLAGGTES 124

Query: 120 MSRAPFVMGKSEQAFGRSAEIF-DTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
           MS  P +  K       +  IF D  IG  +       G GI     TAENVA Q+ +SR
Sbjct: 125 MSMVPMMGHK----IAMNPAIFNDENIGIAY-------GMGI-----TAENVAKQWKVSR 168

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQR------KG---PAKIVEHDEHPRGD 229
             QDAF++ S  +A AA A G    EI    +         +G    ++ ++ DE PR  
Sbjct: 169 EQQDAFSVESHRRALAAQAAGEFNDEISPFALDDHYPNLATRGIVTDSRRIDSDEGPRAG 228

Query: 230 TTLEQLAKLGTPFRQG---GSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMA 286
           TT+E LAKL T FR G   G+VTAGN+S ++DGA A+LLAS  A + + L+  AR VG +
Sbjct: 229 TTMEVLAKLKTVFRNGQFGGTVTAGNSSQMSDGAGAVLLASERAVKEYNLQPLARFVGFS 288

Query: 287 TAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERV 346
            AGV P +MGIGP  A  K L+  GL    +D IELNEAFAAQ LAV+ +LGL  D  +V
Sbjct: 289 VAGVPPEVMGIGPKEAIPKALKQAGLNRDQLDWIELNEAFAAQALAVMGDLGL--DPNKV 346

Query: 347 NPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           NP GGAIALGHPLG +GA  + T +H +  R+ +Y + TMCIG G G A I E +
Sbjct: 347 NPLGGAIALGHPLGATGAVRIATLVHGMRRRKQKYGMVTMCIGTGMGAAGIFEAL 401


Lambda     K      H
   0.319    0.134    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: 448
Number of extensions: 23
Number of successful extensions: 6
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: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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.

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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