Alignments for a candidate for cysK in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Dyella japonica UNC79MFTsu3.2

Align O-ureido-L-serine synthase; Cysteine synthase homolog DscD; O-acetylserine sulfhydrylase; EC 2.6.99.3; EC 2.5.1.47 (characterized)
to candidate N515DRAFT_2767 N515DRAFT_2767 cysteine synthase A

Query= SwissProt::D2Z027
         (324 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2767
          Length = 313

 Score =  432 bits (1112), Expect = e-126
 Identities = 208/310 (67%), Positives = 262/310 (84%)

Query: 3   LFNSILDTIGRTPIVRLQRMAPEHTSVYVKVESFNPGGSVKDRLALSVVLDAEAKGLLKP 62
           +++SILDTIG+TP+V+L R+AP+H  +YVKVE+FNP GSVKDRLAL+++LDAEA+G +KP
Sbjct: 2   IYDSILDTIGKTPVVKLHRLAPKHVELYVKVEAFNPAGSVKDRLALAIILDAEARGTIKP 61

Query: 63  GDTIVECTSGNVGIALAMVAAARGYRFVAVMGDTYSVERRKLIRAYGGKLVLFPGHLGSK 122
           G T+VE TSGN G+ALA V AARGY FVAVM +T+S+ERRKLIRAYGGK++L P      
Sbjct: 62  GQTVVEATSGNTGVALAAVCAARGYPFVAVMTETFSIERRKLIRAYGGKVLLTPAAERGS 121

Query: 123 GGNLIADELAEKYGWFRARQFDNPANPSYHRETTASEILADFAGKRLDHFVTGFGTTGTL 182
           G    A ELA+K+GWF ARQF+NPANP+YHR TTA+EIL DFAG+RLD+FVTG+GT GTL
Sbjct: 122 GMVRKAKELADKHGWFLARQFENPANPAYHRSTTAAEILRDFAGRRLDYFVTGWGTGGTL 181

Query: 183 TGVGQMLRVARPEVRVVALEPSNAAMLARGEWSPHQIQGLAPNFVPGVLDRSVIDDLVTM 242
           TGVG++L+VARPEV+V+A EP+ A++LA  EW PH+IQG  P+FVP VL+R V   ++ +
Sbjct: 182 TGVGEVLKVARPEVKVIASEPAGASLLAGKEWQPHKIQGWTPDFVPAVLNREVAQQILPV 241

Query: 243 DEVTARDTSRRLAAEEGIFAGISAGATVATALSIAEHAPEGTVLLAMLPDTGERYLSTFL 302
           D+V ARDTSR LA +EGIF GIS+GAT+A AL +A+ APEG+VLLAMLPDTGERYLSTFL
Sbjct: 242 DDVVARDTSRALAQKEGIFVGISSGATLAAALQVAKDAPEGSVLLAMLPDTGERYLSTFL 301

Query: 303 FDGVDEGSDD 312
           F+GV+EGSD+
Sbjct: 302 FEGVNEGSDE 311


Lambda     K      H
   0.319    0.136    0.395 

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: 355
Number of extensions: 9
Number of successful extensions: 1
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: 324
Length of database: 313
Length adjustment: 27
Effective length of query: 297
Effective length of database: 286
Effective search space:    84942
Effective search space used:    84942
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate N515DRAFT_2767 N515DRAFT_2767 (cysteine synthase A)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01139.hmm
# target sequence database:        /tmp/gapView.2257073.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.4e-128  413.0   0.0   3.9e-128  412.8   0.0    1.0  1  FitnessBrowser__Dyella79:N515DRAFT_2767  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Dyella79:N515DRAFT_2767  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   0.0  3.9e-128  3.9e-128       2     298 .]       7     302 ..       6     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 3.9e-128
                                TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGia 71 
                                               ++iG+tP+v+L++ +++++e++vk+e +nP++svkdr+ala+i dae +g++k+g+t+veatsGntG+a
  FitnessBrowser__Dyella79:N515DRAFT_2767   7 LDTIGKTPVVKLHRLAPKHVELYVKVEAFNPAGSVKDRLALAIILDAEARGTIKPGQTVVEATSGNTGVA 76 
                                              579**********99999**************************************************** PP

                                TIGR01139  72 lamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfen 141
                                              la v+aargy ++++m et+s+errkl++ayG +++Lt++ae+ +g+++ka+el+++++  ++l++qfen
  FitnessBrowser__Dyella79:N515DRAFT_2767  77 LAAVCAARGYPFVAVMTETFSIERRKLIRAYGGKVLLTPAAERGSGMVRKAKELADKHG--WFLARQFEN 144
                                              ***********************************************************..99******* PP

                                TIGR01139 142 panpeihrkttapeilkdldgk.ldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpg 210
                                              panp++hr+tta+eil+d+ g+ ld fv+g+GtGGt+tGvgevlk ++p++kv+a+ePa +++l+g++++
  FitnessBrowser__Dyella79:N515DRAFT_2767 145 PANPAYHRSTTAAEILRDFAGRrLDYFVTGWGTGGTLTGVGEVLKVARPEVKVIASEPAGASLLAGKEWQ 214
                                              *******************9988*********************************************** PP

                                TIGR01139 211 phkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakklekdkk 280
                                              phkiqG++++f+P+vL++ev ++++ v+d  a +t+r la++eGi+vGissGa++aaal+vak++ ++ +
  FitnessBrowser__Dyella79:N515DRAFT_2767 215 PHKIQGWTPDFVPAVLNREVAQQILPVDDVVARDTSRALAQKEGIFVGISSGATLAAALQVAKDAPEGSV 284
                                              ********************************************************************** PP

                                TIGR01139 281 ivvilpdtgerYlstaLf 298
                                              ++++lpdtgerYlst Lf
  FitnessBrowser__Dyella79:N515DRAFT_2767 285 LLAMLPDTGERYLSTFLF 302
                                              ***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (313 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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