GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Desulfacinum hydrothermale DSM 13146

Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_212636784.1 B9A12_RS01450 6-phosphofructokinase

Query= CharProtDB::CH_024070
         (320 letters)



>NCBI__GCF_900176285.1:WP_212636784.1
          Length = 743

 Score =  240 bits (612), Expect = 9e-68
 Identities = 146/342 (42%), Positives = 197/342 (57%), Gaps = 37/342 (10%)

Query: 1   MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYE--DRMVQLDRYSV 58
           M++ + V+TSGGDAPGMNA +R VVR AL  G++V G++ GY GL    D +  L    V
Sbjct: 1   MVRTMAVMTSGGDAPGMNAGVRAVVRRALDGGMDVYGVFSGYEGLVAGGDAIRPLGWNDV 60

Query: 59  SDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTE--- 115
             ++ RGGTFLG+AR   FR    R  A++NL +RGI ALVVIGGDGS MGA  L E   
Sbjct: 61  GGILPRGGTFLGTARSERFRTVEGRRQAVKNLCERGIQALVVIGGDGSLMGARVLAEEWQ 120

Query: 116 ---------------MGFP----CIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRD 156
                           G P     +GLPG+IDND+ GTD +IG  TAL+ +V AID L  
Sbjct: 121 MHCAELGQEAPAEGRAGMPERLHVVGLPGSIDNDLYGTDMSIGADTALNHIVHAIDDLTS 180

Query: 157 TSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFS---REDLVNEIKAGIAKG 213
           T++SHQR  +VE MGR+CG L L  A+ GG  +V+VPE E      E +   I+   A G
Sbjct: 181 TAASHQRTFIVETMGRHCGYLALMGALGGGASWVLVPEEELDLRWHEKMSRAIERARAIG 240

Query: 214 KKHAIVAITEHMCDVD-------ELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILAS 266
           + H +V + E     D       EL   + +  G + R TVLGH+QRGG P  +DRILA+
Sbjct: 241 RPHQMVVVAEGARHPDGLPIRTEELKRILAERLGIDVRVTVLGHVQRGGPPSAFDRILAT 300

Query: 267 RMGAYAIDLLL-AGYGGRC--VGIQNEQLVHHDIIDAIENMK 305
           R+G  A++LL+ AG    C  VG+Q  ++    + + +E  +
Sbjct: 301 RLGVAAVELLMGAGPEPLCHMVGLQKNRVTTTSLSEVVEKSR 342



 Score =  174 bits (440), Expect = 8e-48
 Identities = 105/283 (37%), Positives = 160/283 (56%), Gaps = 17/283 (6%)

Query: 5   IGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINR 64
           + +LT G DAPGMN A+    R  L +G  V+G+ D + GL       L+   V+  +NR
Sbjct: 389 VAILTGGADAPGMNTAVSIAARCLLNDGYAVLGVRDAFRGLIAADFQPLEWNQVTGWVNR 448

Query: 65  GGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTE-------MG 117
             + LG+AR  E    ++  +A  N++   I  L+ +GG G+Y+ A RL E       + 
Sbjct: 449 PSSELGTARH-ELSGSDLERIA-RNIQAHHIRGLIAVGGLGAYLNAKRLMEGASSHPALA 506

Query: 118 FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDL 177
            P + +P TIDN++  T++TIG  TAL+ +V+A+D++R T+ +++R  VVEVMGR  G L
Sbjct: 507 LPLVLIPATIDNNLPCTEFTIGCDTALNNIVQALDKIRHTAGANRRAFVVEVMGRQSGFL 566

Query: 178 TLAAAIAGGCEFVVVPEVEFSREDLVNEIKA---GIAKGKKHAIVAITEHMC---DVDEL 231
            LA A+A G E   +PE   S  +L  +++A       GK+  I    E+       D +
Sbjct: 567 ALAGALASGAEKAYLPERGISLAELNTDVEALRESFRCGKRMVIYLRNENASRHYTTDFI 626

Query: 232 AHFIEKETG--RETRATVLGHIQRGGSPVPYDRILASRMGAYA 272
           A  +E+E+    + R  +LGH+QRGGSP  +DRILA RMG+ A
Sbjct: 627 ARLLEEESRGLYQVRTAILGHLQRGGSPTAFDRILACRMGSAA 669


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: 683
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 320
Length of database: 743
Length adjustment: 34
Effective length of query: 286
Effective length of database: 709
Effective search space:   202774
Effective search space used:   202774
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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