GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Acidovorax sp. GW101-3H11

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1916
          Length = 399

 Score =  282 bits (721), Expect = 1e-80
 Identities = 172/393 (43%), Positives = 234/393 (59%), Gaps = 6/393 (1%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAG-IDPKEVEDVVMGAAMQQG 61
           +A IV+  RTPIG++ RG    T    LL  AI+ A+ +   +DPK +ED ++G +  +G
Sbjct: 8   DAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGCSFPEG 67

Query: 62  ATGGNIARKAL-LRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
             G N+AR A+ L    PV   G T++R CASG+ A+ +AA  +     ++ + GG ES+
Sbjct: 68  EQGMNMARIAVGLAFNHPV--GGVTVNRFCASGITALQMAADRIRVGEADVLIAGGAESM 125

Query: 121 SLV-QNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
           SLV       +F+A   A +   G  Y   L TAE VA+++ ISRE QD ++LES  R  
Sbjct: 126 SLVPMGGNKPSFNAEVFARDEDVGIAYGMGL-TAEKVAQQWKISREAQDAFALESHLRAI 184

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
            AQ+ G+F DEI P        + ATG V  K  T+S DEGPRP+T+ EGLA LK V   
Sbjct: 185 KAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDTSLEGLAKLKPVFAA 244

Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299
             ++TAGN+SQ SDGA A ++ S+K     GL PL  F    + G  P+ MGIGP+ A+P
Sbjct: 245 RGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIEAIP 304

Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359
             L+  GL  DDIG +ELNEAFA Q L   + LG++P  +N  GGAI++GHP G +GA  
Sbjct: 305 AALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGLNPANVNPMGGAIALGHPLGATGAIR 364

Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           A   +   RR K KY +VTMCVG G G+AG+ E
Sbjct: 365 AATVVHALRRHKLKYGMVTMCVGTGQGAAGIIE 397


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: 440
Number of extensions: 19
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: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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 (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