GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate AO353_25695 AO353_25695 AMP-binding protein

Query= curated2:C1AA44
         (654 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25695
          Length = 554

 Score =  282 bits (721), Expect = 3e-80
 Identities = 193/559 (34%), Positives = 282/559 (50%), Gaps = 58/559 (10%)

Query: 75  LNASVNCIDRHVHGPRRNKAALIWEGEPGDRRTFTYWDLYREVNLAANMLKKLGVGRGDR 134
           LNA V C DRH    R    AL WEG  G   T+T+ DL  +    AN L   GV +GD+
Sbjct: 28  LNACVECCDRHAIPGR---IALFWEGRDGASATYTFSDLQDKAARFANFLLAQGVKKGDK 84

Query: 135 VAIYLPMIPEAVIAMLACARIGAIHTVVFGGFAPESLRDRINDCGCKLLITADGGSRRGQ 194
           VA  LP   E +I + A  RIGA++  +F  F P+++  R+N  G  +++T         
Sbjct: 85  VAGLLPRNVELLIVVFATWRIGAVYQPLFTAFGPKAIEHRLNSSGAAVVVT--------D 136

Query: 195 MVPLKRNADVALKECPSIENVLVVMRRRSGVGDETFAEMQEGRDHWWHRLKRQVPRY--- 251
            V   +  DVA  +CP+I  V          G      +  G   +W  L    P Y   
Sbjct: 137 AVNRPKLNDVA--DCPTIVTV----------GGPKGQGIVRGDFSFWAEL----PNYSAQ 180

Query: 252 CEPEAMDAEDVLFVLYTSGTTGKPKGIVHTTGGFLTGVATTTKYTFDLKEEDVYWCTADI 311
           CEP  +D ED   +++TSGTTG  K +       +    + T+   DL+ ED +W  AD 
Sbjct: 181 CEPVLLDGEDPFLLMFTSGTTGPSKALSVPLKA-IVAFQSYTRDAVDLRPEDAFWNVADP 239

Query: 312 GWITGHSYLVYGPLANGATCVMYEGAPDWPDKDRFWQICERYGVTILYTAPTAIRAFMKW 371
           GW  G  + V GPL+ G     Y+G        R   +  +YG+T L  +PTA R  +  
Sbjct: 240 GWAYGIYFGVTGPLSMGHPITFYDGPFTLESTCR---VINKYGITNLTGSPTAYRLLIAG 296

Query: 372 GTEYVKKHDLSQLRVLGSVGEPINPEAWMWYHEHIGDFQCPIVDTWWQTETGAIMITPLP 431
           G E+ +     +LR++ S GEP+NPE   W+ +++G     I D + QTE G ++     
Sbjct: 297 GDEFARSIK-GKLRIVSSAGEPLNPEVIRWFADNLG---VVIHDHYGQTELGMVLCNHHG 352

Query: 432 GVTTTKPGSATVPFPGIRTALLDANANELTVGG-GLLAITHPWPSMLRTIWGDDQRYVDT 490
              +   G+A    PG R  +LD   NEL+VG  G+LAI      M              
Sbjct: 353 LEHSVHVGAAGFASPGHRIVVLDEAYNELSVGQPGILAIDRTQSPMC------------- 399

Query: 491 YFSKWPGRP------DLYFPGDGAKLDEDGYLWILGRVDDVLNVSGHRIGTMEVESALVD 544
           +F+ + G P      + Y  GD  +L+ DG +  +GR DDV+  SG+R+G  +VESAL++
Sbjct: 400 WFAGYEGAPTKAFVGNYYLSGDTVELNPDGSISFVGRSDDVITTSGYRVGPFDVESALIE 459

Query: 545 HPSVAEAAVVGKHHDLKGQAIAAFVTLRAGFTASGSLRDELRDHVAQKIGALARPDDILF 604
           HP+V EAAV+GK    + + + AFV L A + AS  L +ELR HV +++ A + P +I F
Sbjct: 460 HPAVVEAAVIGKPDPERTELVKAFVVLSAQYRASPELAEELRQHVRKRLAAHSYPREIEF 519

Query: 605 SADLPKTRSGKIMRRLLRD 623
            ++LPKT SGK+ R +LR+
Sbjct: 520 VSELPKTPSGKLQRFILRN 538


Lambda     K      H
   0.320    0.137    0.441 

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: 917
Number of extensions: 49
Number of successful extensions: 8
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: 654
Length of database: 554
Length adjustment: 37
Effective length of query: 617
Effective length of database: 517
Effective search space:   318989
Effective search space used:   318989
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: 53 (25.0 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