GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Pseudomonas fluorescens FW300-N1B4

Align 2-keto-3-deoxy-galactonokinase (characterized, see rationale)
to candidate Pf1N1B4_400 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)

Query= uniprot:B2SYR9
         (350 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_400
          Length = 330

 Score =  305 bits (780), Expect = 1e-87
 Identities = 171/324 (52%), Positives = 210/324 (64%), Gaps = 10/324 (3%)

Query: 26  AALIALDWGTTSLRAYLYDASGNVLATRASTAGIMNLPRSAE-------QGGFDAAFDDT 78
           A LIALDWGTTSLRAY     G VL  R+ ++GIM LPR+           GF+ AFD+ 
Sbjct: 3   AQLIALDWGTTSLRAYKLGFGGQVLEQRSLSSGIMQLPRTPRIIVGQECADGFELAFDEA 62

Query: 79  CGAWLAHAPAAPVIAAGMVGSAQGWLEAPYVDTPASADALVAGIVRVKAACGVTLHIVPG 138
           CG WL   P  PVIA GMVGSAQGW EA Y DTPA+   L   +  V++  GV +HIVPG
Sbjct: 63  CGDWLDAQPDLPVIACGMVGSAQGWREAAYCDTPANVANLGTSLQIVRSLRGVDVHIVPG 122

Query: 139 VLQRGELPNVMRGEETQIFGALGEETNTADSGKRSLIGLPGTHAKWAVVQADRIERFHTF 198
           V+QR  LPNVMRGEETQ+ G L  +   + +G   LIGLPG+H+KW  V    I  F TF
Sbjct: 123 VIQRSRLPNVMRGEETQVLGVL--QHLPSGAGNDLLIGLPGSHSKWVEVADGCIVHFDTF 180

Query: 199 MTGEVFAALREHTILGRTMLTPDSPDTSAFLHGVNIA-REKGQAGVLATVFSSRTLGLTG 257
           MTGEVFA L EH+ILGRT     S +  AF  GV +A    G+ G L+T+FS+R+LGLTG
Sbjct: 181 MTGEVFAVLSEHSILGRTQQRGASFNGEAFDRGVRVALSADGEIGPLSTLFSARSLGLTG 240

Query: 258 QLSREQQPDYLSGLLIGHELAGLDAVLAQQQSALAGQSLRLIGNEALCERYRLALAQFGC 317
           +LS   QPDYLSGLLIGHELA L  V  ++++++   S+ LIGN  LC RY  AL   G 
Sbjct: 241 ELSATAQPDYLSGLLIGHELAALANVQRRRRNSVHLPSIILIGNSQLCARYSRALDACGF 300

Query: 318 TQAELVKHATERGLWRVASQAGLV 341
            +  L + ATERGLW++A  AGL+
Sbjct: 301 ARVTLAEQATERGLWQLAVAAGLI 324


Lambda     K      H
   0.318    0.131    0.384 

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: 344
Number of extensions: 8
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: 350
Length of database: 330
Length adjustment: 28
Effective length of query: 322
Effective length of database: 302
Effective search space:    97244
Effective search space used:    97244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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