GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Herbaspirillum seropedicae SmR1

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS01265 HSERO_RS01265 acetyl-CoA
           acetyltransferase
          Length = 398

 Score =  295 bits (755), Expect = 2e-84
 Identities = 182/411 (44%), Positives = 241/411 (58%), Gaps = 28/411 (6%)

Query: 1   MNDAYICDAIRTPIGRYG-GALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59
           + DAYI  A RTPIG+   G  K+ R DDL    I++ + + PG+D + ++D I GC+  
Sbjct: 5   LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64

Query: 60  AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119
            G    N+AR + LLAGLP    G TINR C SG+ A+  AA  I+ GEA +MIA G ES
Sbjct: 65  EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124

Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRA 179
           M+  P +MG   S      +  D  +G  +             M  TAE VA+Q+ +SR 
Sbjct: 125 MSMVP-MMGFHPSININAFK--DENVGMAY------------GMGLTAEKVAQQWKVSRE 169

Query: 180 DQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIR---------VTLDEHPR-ET 229
            QD F+LAS QKA  AQ  G  A E+   EI ++  +            V+LDE PR ++
Sbjct: 170 AQDEFSLASHQKAIAAQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADS 229

Query: 230 SLESLARLKGVVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGV 289
           +L +LA+LK V    G+VTAGN+S  +DGA AL+I S++  +Q+ L   AR V  A  GV
Sbjct: 230 NLAALAKLKPVFAAKGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGV 289

Query: 290 EPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNG 349
            P IMGIGP  A    L+  G+T DQ+D IELNEAFA+Q LAV+  LGL  D  +VNP G
Sbjct: 290 PPEIMGIGPKEAIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGL--DPSKVNPMG 347

Query: 350 GAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           GAIALGHPLGA+GA    T +H L R N ++ + TMC+G G G A + ER+
Sbjct: 348 GAIALGHPLGATGAIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFERV 398


Lambda     K      H
   0.319    0.134    0.386 

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: 22
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: 400
Length of database: 398
Length adjustment: 31
Effective length of query: 369
Effective length of database: 367
Effective search space:   135423
Effective search space used:   135423
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 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