GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rhaB in Bacteroides thetaiotaomicron VPI-5482

Align Rhamnulokinase; RhaB; EC 2.7.1.5; ATP:L-rhamnulose phosphotransferase; L-rhamnulose 1-kinase; Rhamnulose kinase (uncharacterized)
to candidate 350803 BT1275 L-fuculose kinase (NCBI ptt file)

Query= curated2:Q8A1A3
         (485 letters)



>lcl|FitnessBrowser__Btheta:350803 BT1275 L-fuculose kinase (NCBI
           ptt file)
          Length = 476

 Score =  444 bits (1142), Expect = e-129
 Identities = 223/471 (47%), Positives = 303/471 (64%), Gaps = 5/471 (1%)

Query: 2   KQNFFAVDLGATSGRTILGSFIEGGLNLEEINRFPNHLIEVGGHFYWDIYALYRHIIDGL 61
           +  + AVD G  SGR I GS ++G L LEEI+RF N  +++G H YWD  AL+  +  GL
Sbjct: 6   RNTYLAVDFGGGSGRVIAGSLLQGKLELEEIHRFTNRQVKLGNHVYWDFPALFEDMKTGL 65

Query: 62  KLVAHRGESIASIGIDTWGVDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVY 121
           KL A +G  +  IGIDTWGVDF L+ K GNLL  P  YRD  T G P+  F  +   + Y
Sbjct: 66  KLAAQKGYHVKGIGIDTWGVDFGLIDKKGNLLGNPVCYRDARTDGMPDKVFQILDAQKHY 125

Query: 122 GKTGIQVMNFNSLFQLDTLRRNHDSALEAADKVLFMPDALSYMLTGKMVTEYTIASTAQL 181
             TGIQVM  N+LFQL ++++N D  LE A ++LFMPD  SY LTG    EY IAST++L
Sbjct: 126 ACTGIQVMPINTLFQLYSMQQNQDVLLEVAQRLLFMPDLFSYYLTGVANNEYCIASTSEL 185

Query: 182 VNAHTQRLEPELLKAVGLQEENFGRFVFPGEKIGTLTEEVQKITGLGAIPVIAVAGHDTG 241
           ++A  +    + ++A+GL E  FG  + PG   GTL EE+ + TGLG + +IAV  HDT 
Sbjct: 186 LDARQRNWSMDTIRALGLPEHLFGEIILPGTVRGTLKEEIGRETGLGPVDIIAVGSHDTA 245

Query: 242 SAVAAVPALDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICG 301
           SAVAAVPA +   A+LSSGTWSL+GVE D P++T E     FTNEGGV G IR L+NI G
Sbjct: 246 SAVAAVPATEGQVAFLSSGTWSLLGVEVDEPILTEEARLAQFTNEGGVGGHIRFLQNITG 305

Query: 302 MWLLERCRLNW----GDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRT 357
           +W+L+R    W     + SY  ++ +A   E   ++I  DD  F NP +ME A+  YCR 
Sbjct: 306 LWILQRLMSEWKLRGEEQSYDTILPQAADAE-IDTIIPVDDAEFMNPENMETALLNYCRN 364

Query: 358 TGQPVPEQRGQIVRCIFESLALRYRQVLENLRALSPRPIETLHVIGGGSRNDLLNQFTAN 417
               VP  + ++V+C+ +SLA +YR+ +  L    P PI  L++IGGGS+N LLNQ TAN
Sbjct: 365 HSLKVPGNKAEMVKCVLQSLAFKYREAVAQLNRCLPSPIHRLNIIGGGSQNKLLNQLTAN 424

Query: 418 AIGIPVVAGPSEATAIGNVMIQAMTVGEATDVAGMRQLISRSIPLKTYHPQ 468
           A+GIPV AGP EATA+GN++ QAM  GE + +  +R+++S S+  + Y+P+
Sbjct: 425 ALGIPVYAGPVEATAMGNILTQAMAKGEISSLREIREVVSHSVTPQVYYPE 475


Lambda     K      H
   0.321    0.137    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: 582
Number of extensions: 25
Number of successful extensions: 2
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: 485
Length of database: 476
Length adjustment: 34
Effective length of query: 451
Effective length of database: 442
Effective search space:   199342
Effective search space used:   199342
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 (21.8 bits)
S2: 51 (24.3 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 paper from 2022 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