GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Dyella japonica UNC79MFTsu3.2

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate N515DRAFT_2688 N515DRAFT_2688 acetyl-CoA acyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 N515DRAFT_2688
           acetyl-CoA acyltransferase
          Length = 401

 Score =  281 bits (718), Expect = 3e-80
 Identities = 171/397 (43%), Positives = 230/397 (57%), Gaps = 11/397 (2%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61
           +A IV+  RTP+GKA RG    T    +L H I   + +A GID   + DV++G AM + 
Sbjct: 7   DAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDAHRIGDVIVGCAMPEA 66

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G N+AR  LL AGLP T  G T++R C+SG+QAIA AA  +     ++ +  G ES+S
Sbjct: 67  EQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTESMS 126

Query: 122 LVQNDKMNTFHAVDPAL---EAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRT 178
           +V    M    A++P +   E I   +   M  TAE VAK++ ISRE QD ++  S  R 
Sbjct: 127 MVP--MMGHKVAMNPGIFDNEHI--GIAYGMGITAENVAKQWKISREEQDTFAAASHERA 182

Query: 179 AAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV-- 236
            AA + G+F DEI P        D AT ++      +  DEGPRP +T E L  LK V  
Sbjct: 183 LAAIKAGEFKDEITPFKLDDHYPDLATRSIKTDSRLIDTDEGPRPGSTVEVLGKLKPVFR 242

Query: 237 RGE-GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPV 295
            G+ G ++TAGN+SQ SDGA A ++ S+      GL P+  F      G  PD MGIGP 
Sbjct: 243 NGQFGGSVTAGNSSQTSDGAGAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMGIGPK 302

Query: 296 FAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMS 355
            A+P+ LK+ G++ D +   ELNEAFA Q L     LG+DP K+N  GGAI++GHP G +
Sbjct: 303 EAIPKALKQAGMTQDQLDWIELNEAFAAQSLAVIKDLGLDPSKINPLGGAIALGHPLGAT 362

Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           GA  A   +   RRRK KY +VTMC+G GMG+AG+FE
Sbjct: 363 GAIRAATLVHGMRRRKQKYGMVTMCIGTGMGAAGIFE 399


Lambda     K      H
   0.316    0.134    0.378 

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: 417
Number of extensions: 16
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: 395
Length of database: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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