GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Novosphingobium barchaimii LL02

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_059153516.1 V474_RS22770 thiolase family protein

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_001046635.1:WP_059153516.1
          Length = 378

 Score =  299 bits (766), Expect = 8e-86
 Identities = 184/403 (45%), Positives = 250/403 (62%), Gaps = 28/403 (6%)

Query: 1   MREAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59
           M+   I    R+P    G GAL+ VR DDLAA  +R L+ +     A+ I+D+I+GCA  
Sbjct: 1   MQSVVIAGYARSPFHLAGKGALARVRPDDLAAQVIRGLIGKTGVEPAD-IEDIIVGCAFP 59

Query: 60  AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119
            GE   NVAR+  LLA LP SV G T+NR CGS + A+  A   I  G G++ +  GVES
Sbjct: 60  EGEQGLNVARLIGLLADLPISVGGMTVNRFCGSSMSAIHIAMGQIAIGAGEVFVCAGVES 119

Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTD-SMPETAENVAELLKISR 178
           MSR P +MG            F+        NP +A++      M ETAENVA   +ISR
Sbjct: 120 MSRVP-MMG------------FNP-----LPNPALAKKSAAYMGMGETAENVAAKYQISR 161

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
            DQ++ A+ SQ +   A++ G L++EIVP+  + K G V+E   D  +RPETT E L GL
Sbjct: 162 GDQEALAVESQNKATAARTEGRLSDEIVPI--ETKAGTVSE---DGTIRPETTAEGLAGL 216

Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298
           K  F A G +TAG +S + DGA+A+++ +E  A A GL   ARI ++A +G  P  MGLG
Sbjct: 217 KPAFDAQGSVTAGTSSPLTDGASAVLVTTEDYARAHGLPILARIKSVAISGCAPETMGLG 276

Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358
           P+ ++++ LERAG+S  D+DV+ELNEAFA+QAL  +++LGL  D   VN +GGAIA+GHP
Sbjct: 277 PILSSQKALERAGISAADLDVVELNEAFASQALACIKDLGL--DRAKVNIDGGAIAIGHP 334

Query: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           LG +GAR+   A+  L R  G+YAL + CIG GQGIA +LE V
Sbjct: 335 LGATGARIVGKAASLLKREGGKYALASQCIGGGQGIATVLEAV 377


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: 412
Number of extensions: 16
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: 401
Length of database: 378
Length adjustment: 30
Effective length of query: 371
Effective length of database: 348
Effective search space:   129108
Effective search space used:   129108
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