GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

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 Ac3H11_549 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_549
          Length = 458

 Score =  411 bits (1056), Expect = e-119
 Identities = 207/433 (47%), Positives = 291/433 (67%), Gaps = 9/433 (2%)

Query: 6   DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65
           +T+ +HAG     D   ++ AVPIY T +Y F++++HG+ LF L+VPG +Y+R  NPT++
Sbjct: 35  ETLAVHAGYSP--DPTTKAVAVPIYQTVAYAFDSAQHGADLFDLKVPGNIYTRIMNPTTD 92

Query: 66  VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125
           VLE+R+AALEGG AALAV+SG AA T AIQ +A  GDNIVS S LYGGTYN F  +  + 
Sbjct: 93  VLEKRVAALEGGIAALAVASGMAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQQ 152

Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185
           GI  RF +  +P  F +  D RTKA+++E+IGNP  NV D   I  +AH HG+P++VDNT
Sbjct: 153 GITTRFADPRDPASFAQHIDARTKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIVDNT 212

Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245
                Y  +PI++GADIV HS TK++GGHG ++GG IVDSGKFPW ++  +FP+ ++P  
Sbjct: 213 V-PSPYLLRPIEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEPDV 271

Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305
            YHG +Y EA G  A+I   R   LR+ G  ++P ++FL+LQG+ETL+LR +R  +N L 
Sbjct: 272 SYHGVVYTEALGPAAFIGRARVVPLRNTGAALSPQSAFLILQGIETLALRMDRICDNTLA 331

Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365
           LAK+L+  P V WV Y GL  H  H   ++       G+LSFG+K       + DP + +
Sbjct: 332 LAKYLQSHPKVEWVRYAGLPDHPDHALVQRQSGGKASGILSFGLK-----STDADP-RAA 385

Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425
           GA+ +D L+L + L N+GDAK+L   P  TTH+QLN +E   +GV++ ++R+SVGIE ID
Sbjct: 386 GARFLDALQLFTRLVNIGDAKSLATHPASTTHRQLNPEELAKAGVSESMVRLSVGIEHID 445

Query: 426 DIIADFQQSFETV 438
           D+ AD  Q+ + V
Sbjct: 446 DLRADLVQALDAV 458


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: 565
Number of extensions: 26
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: 458
Length adjustment: 33
Effective length of query: 411
Effective length of database: 425
Effective search space:   174675
Effective search space used:   174675
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