GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucK in Escherichia coli BW25113

Align L-fuculose kinase (characterized, see rationale)
to candidate 17944 b3904 rhamnulokinase (NCBI)

Query= uniprot:G8JZS7
         (476 letters)



>lcl|FitnessBrowser__Keio:17944 b3904 rhamnulokinase (NCBI)
          Length = 489

 Score =  315 bits (806), Expect = 3e-90
 Identities = 188/473 (39%), Positives = 262/473 (55%), Gaps = 11/473 (2%)

Query: 4   TTRNTYLAVDFGGGSGRVIAGSLLQG--KLELEEIHRFTNRQVKLGNHVYWDFPALFEDM 61
           T RN  +AVD G  SGRV+     +    L L EIHRF N       +V WD  +L   +
Sbjct: 2   TFRNC-VAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAI 60

Query: 62  KTGLKLAAQKGYHVKGIGIDTWGVDFGLIDKKGNLLGNPVCYRDARTDGMPDKVFQILDA 121
           + GL    ++G  +  IGIDTWGVDF L+D++G  +G PV YRD+RT+G+  +  Q L  
Sbjct: 61  RLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGK 120

Query: 122 QKHYACTGIQVMPINTLFQLYSMQQNQDVLLEVAQRLLFMPDLFSYYLTGVANNEYCIAS 181
           +  Y  +GIQ +P NTL+QL ++ + Q  L+      L MPD FSY LTG  N EY  A+
Sbjct: 121 RDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNAT 180

Query: 182 TSELLDARQRNWSMDTIRALGLPEHLFGEIILPGTVRGTLKEEIGRETGLGPVDIIAVGS 241
           T++L++    +W    +   G  +  FG    PG V G      G E     + ++AV S
Sbjct: 181 TTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNE-----IPVVAVAS 235

Query: 242 HDTASAVAAVPATEGQVAFLSSGTWSLLGVEVDEPILTEEARLAQFTNEGGVGGHIRFLQ 301
           HDTASAV A P    + A+LSSGTWSL+G E   P   + A  A  TNEGG  G  R L+
Sbjct: 236 HDTASAVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLK 295

Query: 302 NITGLWILQRLMSEWKLRGEEQSYDTILPQAADAEIDTIIPVDDAEFMNPENMETALLNY 361
           NI GLW+LQR++ E ++            QA  A    I P DD  F+NPE M + +   
Sbjct: 296 NIMGLWLLQRVLQEQQINDLPALISA--TQALPACRFIINPNDD-RFINPETMCSEIQAA 352

Query: 362 CRNHSLKVPGNKAEMVKCVLQSLAFKYREAVAQLNRCLPSPIHRLNIIGGGSQNKLLNQL 421
           CR  +  +P + AE+ +C+  SLA  Y + + +L +       +L+I+GGG QN LLNQL
Sbjct: 353 CRETAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQL 412

Query: 422 TANALGIPVYAGPVEATAMGNILTQAMAKGEISSLREIREVVSHSVTPQVYYP 474
            A+A GI V AGPVEA+ +GNI  Q M   E++++ + R+VVS +     + P
Sbjct: 413 CADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTP 465


Lambda     K      H
   0.319    0.136    0.403 

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: 567
Number of extensions: 26
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: 476
Length of database: 489
Length adjustment: 34
Effective length of query: 442
Effective length of database: 455
Effective search space:   201110
Effective search space used:   201110
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 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 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