GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens GW456-L13

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate PfGW456L13_4890 Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4890
          Length = 547

 Score =  241 bits (614), Expect = 7e-68
 Identities = 170/536 (31%), Positives = 271/536 (50%), Gaps = 26/536 (4%)

Query: 19  YSVLTPLLFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSF 77
           Y +L   L L  +G  ++    +VY D  RY+Y T    +   A+AL   G    D ++ 
Sbjct: 16  YPLLIKQLLL--SGVRYEPGREIVYADKLRYSYQTLNKRIRRLANALTAAGVKAGDTVAL 73

Query: 78  ISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVK 137
           +  +   +LE FF VP  G VL  +N RLSP+++ + +NH++   V+V + +L  + ++ 
Sbjct: 74  LDWDSHRYLECFFAVPMIGAVLHTVNIRLSPEQVLFTMNHAEDDLVLVHDDFLPLVEQIH 133

Query: 138 DQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSG 197
            +++     L+  D+ +   T    V   Y  L+   S D    P  +E S+ TL+YT+G
Sbjct: 134 GRLETVKGYLQLTDDEAT--TTSLPVLGEYEHLLSLAS-DQYDFPDFDENSVATLFYTTG 190

Query: 198 TTGLPKGVMHHHRGAFL---NAMAEVLEHQ----MDLNSVYLWTLPMFHAASWGFSWATV 250
           TTG PKGV   HR   L   NA+  +  +Q    +  + VY+   PMFH  +WG  +   
Sbjct: 191 TTGDPKGVYFSHRQLVLHTLNAVGTLGVYQGQPLLRSDDVYMPITPMFHVHAWGVPYVAT 250

Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310
            +G   V   + +   + +L  +E+VT     PT+   + +  +    +F     ML+ G
Sbjct: 251 LMGIKQVYPGRYEPNSLVKLYREEKVTFSHCVPTILQMILNCEEGKATRFDGW-KMLLGG 309

Query: 311 AAPAPATLKAMQEIG--GYMCHV-YGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGI 367
           +A    TL    E    G + H  YG++ET     +   R E   L  E Q  ++ + G 
Sbjct: 310 SA---LTLGVASEANAKGMVVHAGYGMSETCPLLCLTYLRDEDLQLSAEAQLPIRIKTGT 366

Query: 368 PYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427
           P    ++ + DA+G  VP DG+++GE+V+R   +  GY K P+K AE + +GW H+GD A
Sbjct: 367 PVPLVDLKIIDADGNDVPHDGESLGEIVVRAPWLTQGYLKAPDKGAELWHNGWLHTGDMA 426

Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487
            +   G +EI DR KD+I TGGE +SS+ +E  + E PGV +VAV G  DE+WGE   A 
Sbjct: 427 SIDKLGGVEIKDRIKDVIKTGGEWISSLELESLISEHPGVMSVAVVGIADEQWGERPMAM 486

Query: 488 IELQEGV----KLTEEEVIKFCK-ERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537
           +  + G     K+ E  +  F    R+  +  PK  +F   IP T+ GK+ K ++R
Sbjct: 487 VVCEPGQYLDRKILETHLQAFVDGGRINKWAIPKQFKFVAEIPKTSVGKINKKLIR 542


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: 711
Number of extensions: 35
Number of successful extensions: 4
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: 547
Length adjustment: 36
Effective length of query: 513
Effective length of database: 511
Effective search space:   262143
Effective search space used:   262143
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