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_B2623 Synpcc7942_B2623 cysteine synthase A

Query= BRENDA::P9WP55
         (310 letters)



>FitnessBrowser__SynE:Synpcc7942_B2623
          Length = 329

 Score =  315 bits (807), Expect = 9e-91
 Identities = 158/309 (51%), Positives = 215/309 (69%), Gaps = 2/309 (0%)

Query: 3   IAEDITQLIGRTPLVRLRRVTD--GAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGL 60
           I   +T+ IG TPLVRL+      GA+A+++ KLE+ NP  SVKDR  ++++Q+A   GL
Sbjct: 4   ILNRLTEWIGNTPLVRLQETAQQYGAIAEVLLKLEYLNPLGSVKDRTALSLIQSARSQGL 63

Query: 61  IKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGAD 120
           I   T ++EPT+GNTGI LA   AA   R +L MP+ +S ER  L +  GA+++LTP A+
Sbjct: 64  ITAGTTLIEPTTGNTGIGLAFAAAAEQLRLILVMPDRVSAERIRLAKLLGAKVVLTPAAE 123

Query: 121 GMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTG 180
            M G IAKA+ L +      + QQF+NPANP+IH+ TT  E+WRDTDG+VDIVVAGVGTG
Sbjct: 124 AMLGCIAKAQALQQQIPDSVILQQFQNPANPSIHQATTGPEIWRDTDGEVDIVVAGVGTG 183

Query: 181 GTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEI 240
           GT+ G+++ +K  +P  + +AV+PA SPVLSGG  G H + G+G  FV P++D+ L+DEI
Sbjct: 184 GTLMGISRYLKPLRPRLQSIAVQPARSPVLSGGAAGSHQLTGMGPNFVSPLVDRSLIDEI 243

Query: 241 ITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYL 300
           ++   EDA+ V R  A  EG+ +G+SSGA   AALQVA+RPENAGK IV V P   ERYL
Sbjct: 244 LSAYEEDAIAVIRTCAAREGIPLGVSSGAIVWAALQVAKRPENAGKRIVAVCPSGSERYL 303

Query: 301 STPLFADVA 309
           S+ L AD++
Sbjct: 304 SSTLLADIS 312


Lambda     K      H
   0.318    0.136    0.383 

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: 327
Number of extensions: 14
Number of successful extensions: 2
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: 310
Length of database: 329
Length adjustment: 28
Effective length of query: 282
Effective length of database: 301
Effective search space:    84882
Effective search space used:    84882
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Synpcc7942_B2623 Synpcc7942_B2623 (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.17945.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.9e-118  380.0   0.0   4.4e-118  379.8   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_B2623  Synpcc7942_B2623 cysteine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_B2623  Synpcc7942_B2623 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.8   0.0  4.4e-118  4.4e-118       2     297 ..       9     307 ..       8     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.8 bits;  conditional E-value: 4.4e-118
                                  TIGR01139   2 seliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsG 66 
                                                +e iGntPlvrL+    + +a aevl+kle+lnP +svkdr+al++i++a  +gl++ g+t++e+t G
  lcl|FitnessBrowser__SynE:Synpcc7942_B2623   9 TEWIGNTPLVRLQetaQQYGAIAEVLLKLEYLNPLGSVKDRTALSLIQSARSQGLITAGTTLIEPTTG 76 
                                                689*********97545567789********************************************* PP

                                  TIGR01139  67 ntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkyl 134
                                                ntGi+la+ aaa  ++lil+mp+ +s er +l k +Ga++vLt++ae m g+i+ka+ l ++ p++  
  lcl|FitnessBrowser__SynE:Synpcc7942_B2623  77 NTGIGLAFAAAAEQLRLILVMPDRVSAERIRLAKLLGAKVVLTPAAEAMLGCIAKAQALQQQIPDSV- 143
                                                ****************************************************************887. PP

                                  TIGR01139 135 llkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaesp 202
                                                +l+qf+npanp+ih++tt+pei++d+dg++d++vagvGtGGt+ G++++lk  +p ++++av Pa+sp
  lcl|FitnessBrowser__SynE:Synpcc7942_B2623 144 ILQQFQNPANPSIHQATTGPEIWRDTDGEVDIVVAGVGTGGTLMGISRYLKPLRPRLQSIAVQPARSP 211
                                                ******************************************************************** PP

                                  TIGR01139 203 vlsggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalk 270
                                                vlsgg +g+h++ G+g++f+   +d+++ide+++  +e+ai++ r  a++eGi  G+ssGa v+aal+
  lcl|FitnessBrowser__SynE:Synpcc7942_B2623 212 VLSGGAAGSHQLTGMGPNFVSPLVDRSLIDEILSAYEEDAIAVIRTCAAREGIPLGVSSGAIVWAALQ 279
                                                ******************************************************************** PP

                                  TIGR01139 271 vakkle.kdkkivvilpdtgerYlstaL 297
                                                vak++e ++k+iv++ p+ +erYls +L
  lcl|FitnessBrowser__SynE:Synpcc7942_B2623 280 VAKRPEnAGKRIVAVCPSGSERYLSSTL 307
                                                ******9******************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (329 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: 7.06
//
[ok]

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