GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf6N2E2_2190 Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2190
          Length = 565

 Score =  176 bits (447), Expect = 2e-48
 Identities = 153/539 (28%), Positives = 246/539 (45%), Gaps = 41/539 (7%)

Query: 26  LFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPE 84
           +F +   +Y + +  VV   S RYT+    + V + A AL+  G    D+L   + N  +
Sbjct: 29  VFDQTMARYPEGEALVVRHQSLRYTWRQLAEAVDLHARALLALGLKTGDRLGVWAPNCAQ 88

Query: 85  FLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEI 144
           +  S F     G +LV IN      E+ Y++  S  +++V    +  S      Q  A  
Sbjct: 89  WCISQFASAKLGVILVNINPAYRVSELEYVLKQSGCQWLVCAGAFKTSDYHAMLQTLAPE 148

Query: 145 ILLEDPDNPSASETARKEVR-------------MTYRELVKGGSRDPLPIPAKEEYSM-- 189
            L E P     SE    E+R             + + +L   G+       A+ + S+  
Sbjct: 149 -LAEQPIGQMQSERL-PELRGVISLDSQPPSGFLPWSQLAALGAAVTPGQLAERQSSLHF 206

Query: 190 ---ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF- 245
              + + YTSGTTG PKG    H     N         +  +   +  +P++H       
Sbjct: 207 DQPVNIQYTSGTTGFPKGATLSHHNILNNGYMVGESLGLTADDRLVIPVPLYHCFGMVMG 266

Query: 246 SWATVAVGATNVCLDKVDYPLI-YRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRV 304
           +   +  G+T +  +    PL+  + V +E+ T +   PT+++ L D  +R +   S+  
Sbjct: 267 NLGCMTHGSTMIYPNDAFDPLLTLKAVAEEKATALYGVPTMFIALLDQPQRGDFDLSSLR 326

Query: 305 HMLVAGAA-PAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLEEQAK 360
             ++AGA  P     + + E+  +M  V   YG+TET  P S+        + P +E   
Sbjct: 327 TGIMAGATCPIEVMRRVINEM--HMAEVQIAYGMTET-SPVSL-------QTGPTDELEL 376

Query: 361 LKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFR-DG 419
                G      E  + DA G  VP     +GE+  RG++V LGY+ NP+ TA++   DG
Sbjct: 377 RVTTVGRTQPQLESKIIDAAGNLVPRGA--VGELCTRGYSVMLGYWNNPKGTADAIDPDG 434

Query: 420 WFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEK 479
           W H+GD A +   GY+ IV R KD+I  GGE +    +E+     P V  V V G P  +
Sbjct: 435 WMHTGDLATMDEQGYVRIVGRNKDMIIRGGENIYPRELEEFFFTHPAVADVQVIGIPCSR 494

Query: 480 WGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537
           +GE + A I+   G    E+E+  +CKER+AHF+ P+  +F    PMT TGK+QK+ +R
Sbjct: 495 YGEEIVAWIKFHPGHSACEQELQAWCKERIAHFKTPRHFKFVEEFPMTVTGKIQKFRMR 553


Lambda     K      H
   0.319    0.136    0.411 

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: 686
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 549
Length of database: 565
Length adjustment: 36
Effective length of query: 513
Effective length of database: 529
Effective search space:   271377
Effective search space used:   271377
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 (21.7 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