Alignments for a candidate for cysK in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Dinoroseobacter shibae DFL-12

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 3607379 Dshi_0793 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Dino:3607379
          Length = 431

 Score =  348 bits (894), Expect = e-100
 Identities = 195/440 (44%), Positives = 265/440 (60%), Gaps = 15/440 (3%)

Query: 2   PSH-FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQ 60
           PS+ FDT+Q+HAG     D A  +R  PIY TT YVF ++ H + LF L+  GY+YSR  
Sbjct: 6   PSYGFDTLQIHAGARP--DPATGARQTPIYQTTGYVFRDADHAAALFNLQEVGYIYSRLT 63

Query: 61  NPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKI 120
           NPT  VL+ERIA LEGG  A+  SSG AAQ +A+  L   G NIV ++ LYGGT  QF  
Sbjct: 64  NPTVAVLQERIATLEGGVGAVCCSSGHAAQIMALFPLMQPGCNIVVSTRLYGGTVTQFGQ 123

Query: 121 SFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPV 180
           + KRFG  A+FV+ D+ +      D+ T+AV+ E I NP   + D   I  IA   GIP+
Sbjct: 124 TIKRFGWSAKFVDFDDLDAVRAAIDDDTRAVFGEAIANPGGYIMDVRAIADIADAAGIPL 183

Query: 181 VVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQF 240
           ++DNT  A  Y C+PI++GA +V HS TK++ G+GT  GG +VDSGKF W     KFP  
Sbjct: 184 IIDNT-TATPYLCRPIEHGATLVVHSTTKYLTGNGTVTGGCVVDSGKFDWA-ASGKFPSL 241

Query: 241 SQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHG 300
           S+P   YHG  + E +G LA+  H     LRDLG  MNP  +   L G+ETLSLR  RH 
Sbjct: 242 SEPEPAYHGLRFAETFGPLAFTFHGIAVGLRDLGMTMNPQGAHYTLMGIETLSLRMARHV 301

Query: 301 ENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETD 360
           ENA K+AKWLE    V +V+Y GL S  + E  K     G G + +F VK    A     
Sbjct: 302 ENAEKIAKWLEADDRVEFVTYAGLPSSPYFERVKTVCPRGAGALFTFAVKGGYEA----- 356

Query: 361 PFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVG 420
                  ++VD+L++ S++AN+GD ++L+I    TTH+QL  +++ A+G   +++R+S+G
Sbjct: 357 -----CIKLVDSLEIFSHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAAPNVVRLSIG 411

Query: 421 IEFIDDIIADFQQSFETVFA 440
           IE  DD+IAD  Q+     A
Sbjct: 412 IEDADDLIADLDQALSKATA 431


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: 529
Number of extensions: 21
Number of successful extensions: 5
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: 431
Length adjustment: 32
Effective length of query: 412
Effective length of database: 399
Effective search space:   164388
Effective search space used:   164388
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis