GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N1B4

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate Pf1N1B4_4784 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases

Query= curated2:C1AA44
         (654 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4784
          Length = 554

 Score =  270 bits (691), Expect = 1e-76
 Identities = 187/556 (33%), Positives = 274/556 (49%), Gaps = 52/556 (9%)

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

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

Query: 195 MVPLKRNADVALKECPSIENVLVVMRRRSGVGDETFAEMQEGRDHWWHRLKRQVPRYCEP 254
            V   + A+VA  +CP+I  V          G      +  G   +W  L       CEP
Sbjct: 137 AVNRPKLAEVA--DCPTIVTV----------GGPKGQGIVRGDFSFWAELANYSSE-CEP 183

Query: 255 EAMDAEDVLFVLYTSGTTGKPKGIVHTTGGFLTGVATTTKYTFDLKEEDVYWCTADIGWI 314
             +  ED   +++TSGTTG  K +       +    + T+   DL+ ED +W  AD GW 
Sbjct: 184 VLLTGEDPFLLMFTSGTTGPSKALSVPLKA-IVAFQSYTRDAVDLRPEDAFWNVADPGWA 242

Query: 315 TGHSYLVYGPLANGATCVMYEGAPDWPDKDRFWQICERYGVTILYTAPTAIRAFMKWGTE 374
            G  + V GP+A G     Y+G        R   +  +YG+T L  +PTA R  +  G E
Sbjct: 243 YGIYFGVTGPMAMGHPITFYDGPFTLESTCR---VINKYGITNLTGSPTAYRLLIAGGDE 299

Query: 375 YVKKHDLSQLRVLGSVGEPINPEAWMWYHEHIGDFQCPIVDTWWQTETGAIMITPLPGVT 434
           + +     +LR++ S GEP+NPE   W+ +++G     I D + QTE G ++        
Sbjct: 300 FARSIK-GKLRIVSSAGEPLNPEVIRWFADNLG---VVIHDHYGQTELGMVLCNHHGLDH 355

Query: 435 TTKPGSATVPFPGIRTALLDANANELTVGG-GLLAITHPWPSMLRTIWGDDQRYVDTYFS 493
               G+A    PG R  +LD    EL VG  G+LAI      M              +F 
Sbjct: 356 PVHVGAAGFASPGHRIVVLDDEYKELGVGQPGILAIDRTQSPMC-------------WFG 402

Query: 494 KWPGRP------DLYFPGDGAKLDEDGYLWILGRVDDVLNVSGHRIGTMEVESALVDHPS 547
            + G P      + Y  GD  + + DG +  +GR DDV+  SG+R+G  +VESAL++HP+
Sbjct: 403 GYEGAPTKAFVGNYYLSGDTVEWNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPA 462

Query: 548 VAEAAVVGKHHDLKGQAIAAFVTLRAGFTASGSLRDELRDHVAQKIGALARPDDILFSAD 607
           V EAAV+GK    + + + AFV L   + A  +L +ELR HV +++ A A P +I F ++
Sbjct: 463 VVEAAVIGKPDPERTELVKAFVVLSPQYRAEPALAEELRQHVRKRLAAHAYPREIEFVSE 522

Query: 608 LPKTRSGKIMRRLLRD 623
           LPKT SGK+ R +LR+
Sbjct: 523 LPKTPSGKLQRFILRN 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: 931
Number of extensions: 46
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