GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Sphingomonas koreensis DSMZ 15582

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Ga0059261_3284 Ga0059261_3284 acetyl-CoA acetyltransferases

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Korea:Ga0059261_3284
          Length = 391

 Score =  264 bits (675), Expect = 3e-75
 Identities = 175/411 (42%), Positives = 237/411 (57%), Gaps = 34/411 (8%)

Query: 1   MREAFICDGIRTPIGR-YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59
           MR A I    RTPIGR Y GA +++ A  LAA  + E  V+   ++   + DV+ G A Q
Sbjct: 1   MRSAVIVSTARTPIGRAYRGAFNALPAQTLAARSI-EAAVQRAGIEGGEVQDVVFGAALQ 59

Query: 60  AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119
            G    N+AR A L AGLP SVSG +++R C SGL A+  AA+ I   + D+ I GGVES
Sbjct: 60  QGHQAGNIARQAALRAGLPVSVSGMSVDRQCASGLMAIATAAKQIIVDNMDIAIGGGVES 119

Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMP--ETAENVAELLKIS 177
           +S       + A+                  +P +        MP  +TAE VA    IS
Sbjct: 120 ISLVQTPQMRIAA------------------DPELLAMHNDVYMPMLQTAEVVAARYNIS 161

Query: 178 REDQDSFALRSQQRTAKAQSSGILAEEIVPV------VLKNKKGVVTE---IQHDEHLRP 228
           RE QD ++L+SQQRTA AQ++G   +EIVPV      V K  K V  +   +  DE  RP
Sbjct: 162 REVQDEYSLQSQQRTAAAQAAGKFDDEIVPVTATMNIVNKETKEVTQKEVTLTKDEGNRP 221

Query: 229 ETTLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATA 288
           ETTLE L+ L+ P   NGVITAGNAS ++DG+++ ++  E++A  +GLTP  R V MA A
Sbjct: 222 ETTLEGLQALQ-PVVPNGVITAGNASQLSDGSSSSVLMEEKLAEKRGLTPLGRYVGMAVA 280

Query: 289 GVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNP 348
           G +P  MG+GPV A   +LER  L + D+ + ELNEAFA Q L    +LG+P++   +N 
Sbjct: 281 GTKPDEMGIGPVFAIPALLERFNLKMDDIGLWELNEAFAVQVLYCRDKLGIPNEL--LNV 338

Query: 349 NGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399
           NGG+I++GHP GM+GAR    A  E  RR  +Y + TMC+G G G A + E
Sbjct: 339 NGGSISIGHPYGMTGARCTGHALIEGKRRGAKYVVVTMCVGGGMGAAGLFE 389


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: 365
Number of extensions: 16
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 17 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