GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Herbaspirillum seropedicae SmR1

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__HerbieS:HSERO_RS01265
          Length = 398

 Score =  281 bits (720), Expect = 2e-80
 Identities = 175/411 (42%), Positives = 232/411 (56%), Gaps = 27/411 (6%)

Query: 1   MREAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59
           +++A+I    RTPIG+   G   + R DDL    ++  + + P LD + I+D I+GC+  
Sbjct: 5   LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64

Query: 60  AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119
            G    N+AR A LLAGLP ++ G TINR C SG+ A+  AA  I+ G+ D++IA G ES
Sbjct: 65  EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124

Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179
           MS  P +MG   S      +  D  +G  +             M  TAE VA+  K+SRE
Sbjct: 125 MSMVP-MMGFHPSININAFK--DENVGMAY------------GMGLTAEKVAQQWKVSRE 169

Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIV--------PVVLKNKKGVVTE-IQHDEHLRPET 230
            QD F+L S Q+   AQ +G  A+E+         P +   +  V T  +  DE  R ++
Sbjct: 170 AQDEFSLASHQKAIAAQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADS 229

Query: 231 TLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGV 290
            L  L  LK  F A G +TAGN+S  +DGA ALII SE++     LTP AR V+ A  GV
Sbjct: 230 NLAALAKLKPVFAAKGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGV 289

Query: 291 EPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNG 350
            P +MG+GP  A    L+  GL+   +D IELNEAFAAQAL V+ +LGL  D   VNP G
Sbjct: 290 PPEIMGIGPKEAIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGL--DPSKVNPMG 347

Query: 351 GAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           GAIALGHPLG +GA  A    H L R+N +Y + TMC+G G G A I ERV
Sbjct: 348 GAIALGHPLGATGAIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFERV 398


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: 386
Number of extensions: 13
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: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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