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 cysteine synthase (EC 2.5.1.47); O-ureido-L-serine synthase (EC 2.6.99.3) (characterized)
to candidate N515DRAFT_2767 N515DRAFT_2767 cysteine synthase A

Query= BRENDA::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.17518.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  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767  N515DRAFT_2767 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2767  N515DRAFT_2767 cysteine synthase A
   #    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 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGn 67 
                                                   ++iG+tP+v+L++ +++++e++vk+e +nP++svkdr+ala+i dae +g++k+g+t+veatsGn
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767   7 LDTIGKTPVVKLHRLAPKHVELYVKVEAFNPAGSVKDRLALAIILDAEARGTIKPGQTVVEATSGN 72 
                                                  579**********99999************************************************ PP

                                    TIGR01139  68 tGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnky 133
                                                  tG+ala v+aargy ++++m et+s+errkl++ayG +++Lt++ae+ +g+++ka+el+++++  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767  73 TGVALAAVCAARGYPFVAVMTETFSIERRKLIRAYGGKVLLTPAAERGSGMVRKAKELADKHG--W 136
                                                  ***************************************************************..9 PP

                                    TIGR01139 134 lllkqfenpanpeihrkttapeilkdldgk.ldafvagvGtGGtitGvgevlkekkpdikvvaveP 198
                                                  +l++qfenpanp++hr+tta+eil+d+ g+ ld fv+g+GtGGt+tGvgevlk ++p++kv+a+eP
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767 137 FLARQFENPANPAYHRSTTAAEILRDFAGRrLDYFVTGWGTGGTLTGVGEVLKVARPEVKVIASEP 202
                                                  9**************************9988*********************************** PP

                                    TIGR01139 199 aespvlsggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaa 264
                                                  a +++l+g++++phkiqG++++f+P+vL++ev ++++ v+d  a +t+r la++eGi+vGissGa+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767 203 AGASLLAGKEWQPHKIQGWTPDFVPAVLNREVAQQILPVDDVVARDTSRALAQKEGIFVGISSGAT 268
                                                  ****************************************************************** PP

                                    TIGR01139 265 vaaalkvakklekdkkivvilpdtgerYlstaLf 298
                                                  +aaal+vak++ ++ +++++lpdtgerYlst Lf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2767 269 LAAALQVAKDAPEGSVLLAMLPDTGERYLSTFLF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.22
//
[ok]

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:

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, or view the source code, or see 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