GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Streptacidiphilus oryzae TH49

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_037568740.1 BS73_RS02005 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000744815.1:WP_037568740.1
          Length = 532

 Score =  417 bits (1072), Expect = e-121
 Identities = 227/526 (43%), Positives = 322/526 (61%), Gaps = 27/526 (5%)

Query: 19  YSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFI 78
           +  LTP+ +L+RA     D+TAVV    R+TY+  +D     A AL     +R   ++ +
Sbjct: 13  FEPLTPVSYLDRAAAAHGDRTAVVDGGRRWTYAQLHDRCRRLAGALAP--LARNRPVAVL 70

Query: 79  SRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKD 138
           + N    LE+ FGVP+AG  LVP+N RL+  E+A I+ HS++  ++ D  +   + +   
Sbjct: 71  APNTHVMLEAHFGVPWAGVPLVPVNTRLAAGEVARILEHSEAAVLIHDPAFDEVVADALA 130

Query: 139 QIKAEIILLEDPDNPSASETARKEVRMTYRELVKG---GSRDPLPIPAKEEYSMITLYYT 195
           ++ A  +L+   +               Y  L+ G   G+R P      +E ++++L YT
Sbjct: 131 RLDAPPVLVRAGEG--------------YERLLAGAEPGARTPA-----DERALLSLNYT 171

Query: 196 SGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGAT 255
           SGTTG PKGVM+HHRGA+L A+A V    +  ++V+LWTLPMFH   W F WA  A  AT
Sbjct: 172 SGTTGRPKGVMYHHRGAYLQALAMVGHTGLSPSAVHLWTLPMFHCNGWCFPWAVTAAAAT 231

Query: 256 NVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAP 315
           +VCL +V+   ++RL+ +E VTH+  APTV   LA   +   L    RV     GA P+P
Sbjct: 232 HVCLPRVEPAEVWRLIREEGVTHLNGAPTVLSMLAYAPEAGPLPHPVRV--ATGGAPPSP 289

Query: 316 ATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP-YVSFEM 374
           A L+ M E+G  + H+YGLTET+GP  +C+WR EWD L    QA+LKARQG+   ++ + 
Sbjct: 290 AILRRMGELGFEVTHLYGLTETFGPAMLCDWRPEWDGLDAGAQARLKARQGVGNMIACQA 349

Query: 375 DVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGY 434
            V   +G  VP DG  +GE+ +RG+NV LGY+K+PE TA++  DGWF +GD  V HPDGY
Sbjct: 350 RVVAKDGGEVPADGTAVGEIALRGNNVMLGYFKDPEATAQAAPDGWFRTGDLGVRHPDGY 409

Query: 435 IEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGV 494
           IE+ DR KD+I +GGE ++S+ VE+ L E P V   AV   P EKWGEV  A + L EG 
Sbjct: 410 IELRDRSKDIIVSGGENIASVEVEQALAEHPAVLEAAVVAAPHEKWGEVPVAYVALHEGA 469

Query: 495 KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEA 540
             T +E+I F +ERLAHF+ P+ V FGP+P T+TGK+QK+VLR+ A
Sbjct: 470 AATADELIAFVRERLAHFKAPESVCFGPLPKTSTGKIQKFVLRDRA 515


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: 744
Number of extensions: 30
Number of successful extensions: 5
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: 549
Length of database: 532
Length adjustment: 35
Effective length of query: 514
Effective length of database: 497
Effective search space:   255458
Effective search space used:   255458
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: 52 (24.6 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