GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Gallaecimonas xiamenensis 3-C-1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_008484014.1 B3C1_RS07740 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000299915.1:WP_008484014.1
          Length = 558

 Score =  167 bits (424), Expect = 7e-46
 Identities = 153/555 (27%), Positives = 254/555 (45%), Gaps = 62/555 (11%)

Query: 23  TPLL------FLERAGKYFKDKTAVVYRDS--RYTYSTFYDNVMVQASALMRRGFSREDK 74
           TPLL       L+       D  A+V R    R++YS   + V   A +L+R G  + D+
Sbjct: 14  TPLLNMTIGDCLKEKATLHPDHPALVVRHQQIRWSYSQLLEQVDRLAISLLRLGIEKGDR 73

Query: 75  LSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNS-L 133
           +   + N  ++L   F     G ++V IN      E+AY +N    K ++  E +  S  
Sbjct: 74  VGIWAPNCYQWLLVQFATARLGAIMVCINPNYQKSELAYALNKVQCKALICAEGFRQSNY 133

Query: 134 LEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSR----------------- 176
           L + + +  E+         S +E   + +      +  G +R                 
Sbjct: 134 LAMLEALAPELA-----HTHSGAELDAQALPSLRHIITMGKARPGYLAFDWLMGDLTAED 188

Query: 177 ----DPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYL 232
               D L +  ++    I + +TSGTTG PKG    H     NA        M       
Sbjct: 189 SALLDALDLSPQDP---INIQFTSGTTGNPKGATLSHHNILNNAKLVGDAMGMSPADKLC 245

Query: 233 WTLPMFHAASWGF-SWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCAAPTVYVNLA 290
             +P++H       S   VA GAT V   +  D     + V +ER T +   PT+++   
Sbjct: 246 IPVPLYHCFGMVLGSLLCVAHGATAVFPAEAFDADSTLKAVSEERCTALHGVPTMFIAEL 305

Query: 291 DYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHV------YGLTETYGPHSIC 344
           ++ + +    ++    ++AGA      ++ M+++ G + H+      YG TE+  P +  
Sbjct: 306 EHPQFDQFDLTSLRTGVMAGAT---CPVELMKKVIGKL-HMEEVLIAYGQTES-SPINHI 360

Query: 345 EWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALG 404
             R +    PLE++     + G      E+ + DA G  VP   +  GE+  R ++V LG
Sbjct: 361 TLRDD----PLEKRIGTVGKAGAHQ---EVKIVDAFGDEVPLGER--GEICNRAYSVMLG 411

Query: 405 YYKNPEKTAESF-RDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLME 463
           Y+ +P+K+AE+  +DGW HSGD  V+  DGY+++V R KD+I  GGE +    +E+    
Sbjct: 412 YWDDPQKSAETVDQDGWLHSGDLGVMDQDGYVQVVGRIKDMIIRGGENIYPREIEEFYYR 471

Query: 464 IPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GP 522
            P V+ + V+G PD+K+GE V A + L+ G +   EE+  F +  L+HF+ P+   F   
Sbjct: 472 HPKVQDIQVFGIPDDKYGEQVCAWVMLRSGQQADAEEMRAFAEGELSHFKIPRHFHFVDN 531

Query: 523 IPMTATGKMQKYVLR 537
            PMT TGK+QK+ +R
Sbjct: 532 YPMTVTGKIQKFRMR 546


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: 671
Number of extensions: 35
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: 558
Length adjustment: 36
Effective length of query: 513
Effective length of database: 522
Effective search space:   267786
Effective search space used:   267786
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 24 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