GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Chryseobacterium viscerum 687B-08

Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_103233592.1 C1634_RS09815 6-phosphofructokinase

Query= CharProtDB::CH_024070
         (320 letters)



>NCBI__GCF_002899945.2:WP_103233592.1
          Length = 328

 Score =  239 bits (609), Expect = 9e-68
 Identities = 137/305 (44%), Positives = 193/305 (63%), Gaps = 4/305 (1%)

Query: 2   IKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDM 61
           +KKI VLTSGGD+PGMNAA+R VVR+A    +E  G+ +GY GL  D  +++   SV ++
Sbjct: 6   VKKIAVLTSGGDSPGMNAALRAVVRTANYYNIECYGVREGYNGLINDDFLKMGARSVKNI 65

Query: 62  INRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLT-EMGFPC 120
           IN+GGT L SAR  EFR +  R  A +N  K GID LV IGGDG++ GA     E G   
Sbjct: 66  INQGGTILKSARSAEFRTKEGRQKAYDNCVKLGIDGLVCIGGDGTFTGAKIFNEEFGIRV 125

Query: 121 IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA 180
           IG+PGTIDNDI GTD TIG+ TAL+T ++AID++RDT++SH R+  VEVMGR  G + L 
Sbjct: 126 IGIPGTIDNDIFGTDNTIGYDTALNTAMDAIDKIRDTATSHNRVFFVEVMGRDAGFIALN 185

Query: 181 AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAIT--EHMCDVDELAHFIEKE 238
           + +A G   +++PE + S ++L  + +     GK  +IV +   E + +V ELA   +  
Sbjct: 186 SGLATGALDILIPEKKDSIDELFAKFRNAEKTGKSSSIVVVAEGEKLANVYELAEKTKLT 245

Query: 239 -TGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDI 297
               + R  +LGH+QRGGSP   DR+LASR+G  A+  L+ G      G+++  L +  I
Sbjct: 246 FPDYDIRVAILGHMQRGGSPSCADRVLASRLGYGAVVGLMDGQSNVMAGMRSNDLTYTPI 305

Query: 298 IDAIE 302
            +AI+
Sbjct: 306 EEAIK 310


Lambda     K      H
   0.322    0.141    0.413 

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: 319
Number of extensions: 15
Number of successful extensions: 3
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: 320
Length of database: 328
Length adjustment: 28
Effective length of query: 292
Effective length of database: 300
Effective search space:    87600
Effective search space used:    87600
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 (21.9 bits)
S2: 48 (23.1 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