GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas putida KT2440

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate PP_2528 PP_2528 O-acetylhomoserine (thiol)-lyase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Putida:PP_2528
          Length = 425

 Score =  412 bits (1058), Expect = e-119
 Identities = 210/431 (48%), Positives = 284/431 (65%), Gaps = 13/431 (3%)

Query: 6   DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65
           +T+ +HAG     D   ++ AVPIY TTS+ F++++HG+ LF L+V G +YSR  NPT++
Sbjct: 4   ETLAIHAGFSP--DPTTKAVAVPIYQTTSFAFDDTQHGADLFDLKVAGNIYSRIMNPTND 61

Query: 66  VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125
           VLE+R+AALEGG  ALAV+SG AA T AIQ +A  GDNIVS + LYGGTYN    +  R 
Sbjct: 62  VLEQRMAALEGGVGALAVASGMAAITYAIQTVAEAGDNIVSVAKLYGGTYNLLAHTLPRM 121

Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185
           GI  RF   D+    E + D RTKAV+ E+IGNP  N+ D   +   AH+HG+P++VDNT
Sbjct: 122 GIHTRFAAHDDIAALEALIDARTKAVFCESIGNPAGNIVDIAALAEAAHRHGVPLIVDNT 181

Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245
             A    C+P ++GADIV HS TK+IGGHGT+IGGI++DSGKFPW +  E+F   + P  
Sbjct: 182 V-ATPVLCRPFEHGADIVVHSLTKYIGGHGTSIGGIVIDSGKFPWAENKERFALLNTPDP 240

Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305
            YHG  Y EA+G  A+I   R   LR+ G  ++PF +FL+LQG+ETL+LR ERH ENALK
Sbjct: 241 SYHGVTYTEAFGPAAFIGRCRVVPLRNTGAALSPFNAFLILQGLETLALRMERHTENALK 300

Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365
           +A +L+    V+WV + GL  H  H  A++Y       +LSFG+K            + +
Sbjct: 301 VAHYLQAHEQVAWVKFAGLPDHPEHALAQRYTGGKPASILSFGIKG----------GQAA 350

Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425
           GA+ +D L+L   L N+GDAK+L   P  TTH+QLND E   +GV +D++R+S+GIE  D
Sbjct: 351 GARFIDALQLVVRLVNIGDAKSLACHPASTTHRQLNDDELEKAGVPRDMVRLSIGIEHSD 410

Query: 426 DIIADFQQSFE 436
           DIIAD  Q+ E
Sbjct: 411 DIIADLAQALE 421


Lambda     K      H
   0.317    0.136    0.402 

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: 538
Number of extensions: 23
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: 444
Length of database: 425
Length adjustment: 32
Effective length of query: 412
Effective length of database: 393
Effective search space:   161916
Effective search space used:   161916
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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