Alignments for a candidate for cysK in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Clostridium kluyveri DSM 555

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_012103744.1 CKL_RS16605 cysteine synthase A

Query= BRENDA::P37887
         (308 letters)



>NCBI__GCF_000016505.1:WP_012103744.1
          Length = 303

 Score =  353 bits (905), Expect = e-102
 Identities = 177/303 (58%), Positives = 231/303 (76%), Gaps = 3/303 (0%)

Query: 4   VANSITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLK 63
           + N+  ++IG TP+ KL+   +++SA++Y+KLE  NPG S+KDR  L MIE AEK+G ++
Sbjct: 2   IFNNAIDMIGATPLFKLDNFKNKDSAEIYVKLEKYNPGGSIKDRAALGMIEKAEKDGLIE 61

Query: 64  AGNTIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGM 123
            G TI+EPTSGNTGI LAM+   KG K I+VMP+TMS+ERRN+++AYGAELVLT G +GM
Sbjct: 62  KGGTIVEPTSGNTGIALAMIGKLKGYKVIIVMPETMSVERRNMIKAYGAELVLTDGTKGM 121

Query: 124 KGAIKKAEELAE-KHGYFVPQQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTGG 182
           KGAI+KA E+A+ K GY++PQQF N +NP+ H +TT +EI+E      +DAFVAG+GT G
Sbjct: 122 KGAIEKAYEIAKNKRGYYIPQQFINKANPKKHYETTAEEILEDL--QHVDAFVAGVGTAG 179

Query: 183 TITGAGEVLKEAYPSIKIYAVEPSDSPVLSGGKPGPHKIQGIGAGFVPDILNTEVYDEIF 242
           T+ G GE LK    ++KI AVEP+ SPVLSGG+ G HKIQGIGAGFVPDI   E+ D+I 
Sbjct: 180 TLAGVGENLKGRDKNVKIIAVEPASSPVLSGGQTGAHKIQGIGAGFVPDIYIPELVDKII 239

Query: 243 PVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSNGERYLST 302
            + +E AF+YAR   +EEGIL GISSGA I AA+QVA++LGKGKKV+ + P  GE+YLS 
Sbjct: 240 TITDETAFKYARLMGKEEGILVGISSGANIAAAIQVAEELGKGKKVVTVAPDGGEKYLSM 299

Query: 303 PLY 305
            LY
Sbjct: 300 GLY 302


Lambda     K      H
   0.313    0.134    0.373 

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: 283
Number of extensions: 14
Number of successful extensions: 3
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: 308
Length of database: 303
Length adjustment: 27
Effective length of query: 281
Effective length of database: 276
Effective search space:    77556
Effective search space used:    77556
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_012103744.1 CKL_RS16605 (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.650148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-130  418.8   5.7   6.8e-130  418.6   5.7    1.0  1  NCBI__GCF_000016505.1:WP_012103744.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_012103744.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.6   5.7  6.8e-130  6.8e-130       3     298 .]       8     302 ..       6     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 418.6 bits;  conditional E-value: 6.8e-130
                             TIGR01139   3 eliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 
                                           ++iG tPl +L+  +++ +ae++vkle+ nP++s+kdr+al mie+aek+gl++kg tive+tsGntGialam
  NCBI__GCF_000016505.1:WP_012103744.1   8 DMIGATPLFKLDnFKNKDSAEIYVKLEKYNPGGSIKDRAALGMIEKAEKDGLIEKGGTIVEPTSGNTGIALAM 80 
                                           68*********9899999******************************************************* PP

                             TIGR01139  75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpei 147
                                           ++  +gyk+i++mpetms+err+++kayGaelvLtdg++gmkgaieka e+++++   y +++qf n+anp+ 
  NCBI__GCF_000016505.1:WP_012103744.1  81 IGKLKGYKVIIVMPETMSVERRNMIKAYGAELVLTDGTKGMKGAIEKAYEIAKNKRGYY-IPQQFINKANPKK 152
                                           *****************************************************999555.************* PP

                             TIGR01139 148 hrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigag 220
                                           h +tta+eil+dl+ ++dafvagvGt Gt++Gvge lk  ++++k++avePa+spvlsgg++g+hkiqGigag
  NCBI__GCF_000016505.1:WP_012103744.1 153 HYETTAEEILEDLQ-HVDAFVAGVGTAGTLAGVGENLKGRDKNVKIIAVEPASSPVLSGGQTGAHKIQGIGAG 224
                                           ************96.6********************************************************* PP

                             TIGR01139 221 fiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakklekdkkivvilpdtgerYl 293
                                           f+P++   e++d++i+++de+a+++ar + keeGilvGissGa++aaa++va++l+k+kk+v+++pd ge+Yl
  NCBI__GCF_000016505.1:WP_012103744.1 225 FVPDIYIPELVDKIITITDETAFKYARLMGKEEGILVGISSGANIAAAIQVAEELGKGKKVVTVAPDGGEKYL 297
                                           ************************************************************************* PP

                             TIGR01139 294 staLf 298
                                           s+ L+
  NCBI__GCF_000016505.1:WP_012103744.1 298 SMGLY 302
                                           *9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (303 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: 19.49
//
[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