GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AO356_01575 AO356_01575 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01575 AO356_01575
           AMP-binding protein
          Length = 565

 Score =  168 bits (426), Expect = 4e-46
 Identities = 149/539 (27%), Positives = 244/539 (45%), Gaps = 41/539 (7%)

Query: 26  LFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPE 84
           +F +   +Y + +  VV   S RYT+    + V + A AL+  G    D+L   + N  +
Sbjct: 29  VFDQTVARYPEGEALVVRHQSLRYTWQQLAEAVDLHARALLALGLKTGDRLGVWAPNCAQ 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-PELRGVISLDSQPPAGFLPWSQLAALGAAVTPGQLAERQSSLRF 206

Query: 190 ---ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF- 245
              + + YTSGTTG PKG    H     N         +      +  +P++H       
Sbjct: 207 DQPVNIQYTSGTTGFPKGATLSHHNILNNGYMVGESLGLTAGDRLVIPVPLYHCFGMVMG 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-------QTGPSDELEL 376

Query: 361 LKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFR-DG 419
                G      E  + D  G  V      +GE+  RG++V LGY+ NP+ T+++   +G
Sbjct: 377 RVTTVGRTQPQLESKIIDEAGNLV--SRGAVGELCTRGYSVMLGYWNNPKGTSDAIDPEG 434

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

Query: 480 WGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537
           +GE + A I+   G   +E+E+  +CKER+AHF+ P+  +F    PMT TGK+QK+ +R
Sbjct: 495 YGEEIVAWIKFHPGHSASEQELQAWCKERIAHFKTPRHFKFVEEFPMTVTGKIQKFRMR 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: 677
Number of extensions: 32
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 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, the preprint on GapMind for carbon sources, 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