Alignments for a candidate for cysK in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Synechococcus elongatus PCC 7942

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Synpcc7942_1466 Synpcc7942_1466 cysteine synthase

Query= BRENDA::A8YBP8
         (315 letters)



>FitnessBrowser__SynE:Synpcc7942_1466
          Length = 334

 Score =  471 bits (1213), Expect = e-138
 Identities = 235/312 (75%), Positives = 271/312 (86%)

Query: 1   MLIARDITQLVGRTPLVQLNRIPVAEGVKARIVVKLESMNPAASVKDRIGVSMVEDAEAA 60
           M IA++IT+L+GRTPLVQLNRIPVA+G  ARIVVKLES NP+ASVKDRIG+SM+ +AE  
Sbjct: 15  MRIAQNITELIGRTPLVQLNRIPVADGCLARIVVKLESFNPSASVKDRIGISMILEAERK 74

Query: 61  GLIHPDKTILVEPTSGNTGIALAMVAAAKGYRLVLTMPETMSLERRAMLKAYGAQLELTP 120
           GLI PD+T LVEPTSGNTGIALAM AAA+GYRL+LTMP+TMS ERRAML+AYGA LELTP
Sbjct: 75  GLIAPDRTTLVEPTSGNTGIALAMAAAARGYRLILTMPDTMSSERRAMLRAYGATLELTP 134

Query: 121 GSQGMEGAITRAEEIVENTPNAYSLQQFRNPANPKIHRETTAEEIWADTDGLVDIVIGGV 180
           G +GM G I RA+EIV + P AY LQQF+NPANPKIHRETTAEEIWADTDG VDI+I GV
Sbjct: 135 GIEGMAGCIQRAQEIVASHPEAYMLQQFKNPANPKIHRETTAEEIWADTDGTVDILISGV 194

Query: 181 GTGGTITGIAETIKPRRPQFQAIAVEPSNSPVLSGGQPGPHKIQGIGAGFIPAIFRPELI 240
           GTGGTITG+AE +K R+P FQA AVEP+NSPVLSGG+PGPHKIQGIGAGF+P +   +LI
Sbjct: 195 GTGGTITGVAEVLKERKPSFQAFAVEPANSPVLSGGRPGPHKIQGIGAGFVPEVLATQLI 254

Query: 241 DEVIIVDDTEAFAYARRLARQEGLLSGISAGAALWAAIQVGKRPENEDKLIVMIQPSFGE 300
           DEV+ V D EA AY RRLAR+EGLLSGIS+GAA+ AA+QV +RPEN DKLIV+I PSFGE
Sbjct: 255 DEVVTVSDDEAIAYGRRLAREEGLLSGISSGAAVAAAVQVARRPENTDKLIVVILPSFGE 314

Query: 301 RYLSTALFKDLE 312
           RYLST LF++ E
Sbjct: 315 RYLSTPLFQEPE 326


Lambda     K      H
   0.317    0.135    0.379 

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: 399
Number of extensions: 11
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: 315
Length of database: 334
Length adjustment: 28
Effective length of query: 287
Effective length of database: 306
Effective search space:    87822
Effective search space used:    87822
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: 48 (23.1 bits)

Align candidate Synpcc7942_1466 Synpcc7942_1466 (cysteine synthase)
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.23805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-148  478.5   0.1   4.6e-148  478.3   0.1    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1466  Synpcc7942_1466 cysteine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1466  Synpcc7942_1466 cysteine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.3   0.1  4.6e-148  4.6e-148       1     298 []      21     322 ..      21     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 478.3 bits;  conditional E-value: 4.6e-148
                                 TIGR01139   1 iseliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveats 65 
                                               i+eliG+tPlv+Ln   +a+++ a+++vkles+nPs+svkdri+++mi +ae++gl+ +++ t+ve+ts
  lcl|FitnessBrowser__SynE:Synpcc7942_1466  21 ITELIGRTPLVQLNripVADGCLARIVVKLESFNPSASVKDRIGISMILEAERKGLIAPDRtTLVEPTS 89 
                                               689***********9888999**************************************9879****** PP

                                 TIGR01139  66 GntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkyl 134
                                               GntGialam aaargy+liltmp+tms err++l+ayGa l Lt+g egm+g+i++a+e+v+++p++y 
  lcl|FitnessBrowser__SynE:Synpcc7942_1466  90 GNTGIALAMAAAARGYRLILTMPDTMSSERRAMLRAYGATLELTPGIEGMAGCIQRAQEIVASHPEAY- 157
                                               ********************************************************************. PP

                                 TIGR01139 135 llkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespv 203
                                               +l+qf+npanp+ihr+tta+ei+ d+dg++d++++gvGtGGtitGv+evlke kp+++++avePa+spv
  lcl|FitnessBrowser__SynE:Synpcc7942_1466 158 MLQQFKNPANPKIHRETTAEEIWADTDGTVDILISGVGTGGTITGVAEVLKERKPSFQAFAVEPANSPV 226
                                               ********************************************************************* PP

                                 TIGR01139 204 lsggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkva 272
                                               lsgg+pgphkiqGigagf+P+vL +++idev++vsd+eai+++rrla+eeG+l+GissGaavaaa++va
  lcl|FitnessBrowser__SynE:Synpcc7942_1466 227 LSGGRPGPHKIQGIGAGFVPEVLATQLIDEVVTVSDDEAIAYGRRLAREEGLLSGISSGAAVAAAVQVA 295
                                               ********************************************************************* PP

                                 TIGR01139 273 kkle.kdkkivvilpdtgerYlstaLf 298
                                               +++e +dk+ivvilp++gerYlst+Lf
  lcl|FitnessBrowser__SynE:Synpcc7942_1466 296 RRPEnTDKLIVVILPSFGERYLSTPLF 322
                                               ***99*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (334 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: 10.08
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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