GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas stutzeri RCH2

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 GFF3618 Psest_3685 OAH/OAS sulfhydrylase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__psRCH2:GFF3618
          Length = 425

 Score =  431 bits (1107), Expect = e-125
 Identities = 220/429 (51%), Positives = 292/429 (68%), Gaps = 13/429 (3%)

Query: 6   DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65
           +T+ +HAG     D   R+ AVPIY TTSY F++++HG+ LF L+VPG +Y+R  NPT++
Sbjct: 4   ETLAIHAGYSP--DPTTRAVAVPIYQTTSYAFDDTQHGADLFDLKVPGNIYTRIMNPTTD 61

Query: 66  VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125
           VLE+R+AALEGG AALAV+SG AA T AIQ +A  GDNIVS + LYGGTYN F  +  R 
Sbjct: 62  VLEQRVAALEGGVAALAVASGMAAITYAIQTIAEVGDNIVSVAKLYGGTYNLFAHTLPRQ 121

Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185
           GIE RF   D+    E + DERTKAV+ E+IGNP  NV D   +   AH+HG+P++VDNT
Sbjct: 122 GIEVRFAAHDDIAALESLIDERTKAVFCESIGNPAGNVIDLAALAEAAHRHGVPLIVDNT 181

Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245
             A    C+P ++GADIV HS TK++GGHGT+IGGI+VDSGKFPW  + ++F   + P  
Sbjct: 182 V-ATPMLCRPFEHGADIVVHSLTKYMGGHGTSIGGIVVDSGKFPWAQHKKRFALLNTPDV 240

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

Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365
           +A++L+  P V+WV Y GL  H  HE A++Y+      +L FG++    A          
Sbjct: 301 VAEFLQAHPQVAWVKYAGLPDHPEHELARRYMGGTPASILCFGIEGGIEA---------- 350

Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425
           GA+ +D LKL   L N+GDAK+L   P  TTH+QLN  E   +GV++DLIR+S+GIE ID
Sbjct: 351 GARFIDALKLVVRLVNIGDAKSLACHPASTTHRQLNADELARAGVSQDLIRLSIGIEHID 410

Query: 426 DIIADFQQS 434
           DI+AD  Q+
Sbjct: 411 DILADLAQA 419


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: 542
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