Alignments for a candidate for cysK in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Methanobacterium lacus AL-21

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_013644774.1 METBO_RS05910 cysteine synthase A

Query= BRENDA::P9WP55
         (310 letters)



>NCBI__GCF_000191585.1:WP_013644774.1
          Length = 328

 Score =  393 bits (1010), Expect = e-114
 Identities = 195/307 (63%), Positives = 245/307 (79%), Gaps = 1/307 (0%)

Query: 3   IAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIK 62
           IA DIT+ IG TPLVRL ++T+G+ A+++ K+E FNP +SVKDRIGVAM++A E+AG+IK
Sbjct: 11  IANDITETIGNTPLVRLNKLTEGSKAEVLVKVESFNPLSSVKDRIGVAMIEAGEEAGVIK 70

Query: 63  PDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGM 122
            +TI++EPTSGNTGIALA V AA+GY+ +LTMP+TMS+ERR LL   GAE++LTPGA+GM
Sbjct: 71  ENTILIEPTSGNTGIALAFVAAAKGYKLILTMPDTMSIERRKLLALLGAEIVLTPGANGM 130

Query: 123 SGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGT 182
            GA+AKAEELA       +PQQF+N ANP IHR TTA+E+WRDTDGKVD++V+G GTGGT
Sbjct: 131 PGAVAKAEELAAEIPGAVMPQQFKNIANPKIHRETTAQEIWRDTDGKVDVLVSGTGTGGT 190

Query: 183 ITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIIT 242
           ITGVA  +KE KP  + VAVEP  SPVLSGG  GPH IQGIG GF+P VL  +++DEI+ 
Sbjct: 191 ITGVATALKELKPEFKAVAVEPVTSPVLSGGSPGPHKIQGIGPGFIPDVLQTEIIDEIVQ 250

Query: 243 VGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLST 302
           V ++DA     +LAREEG+L GISSGAA  AALQ+A++ E AGK IVV+LPD GERYLS 
Sbjct: 251 VSDDDAAQTLLKLAREEGILAGISSGAAVFAALQLAKKDEYAGKQIVVILPDTGERYLSM 310

Query: 303 P-LFADV 308
             +F D+
Sbjct: 311 DWVFEDI 317


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: 330
Number of extensions: 7
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: 310
Length of database: 328
Length adjustment: 28
Effective length of query: 282
Effective length of database: 300
Effective search space:    84600
Effective search space used:    84600
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 WP_013644774.1 METBO_RS05910 (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.1428570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-143  461.4   2.5   7.4e-143  461.2   2.5    1.0  1  NCBI__GCF_000191585.1:WP_013644774.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000191585.1:WP_013644774.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.2   2.5  7.4e-143  7.4e-143       1     296 [.      15     311 ..      15     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 461.2 bits;  conditional E-value: 7.4e-143
                             TIGR01139   1 iseliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGial 72 
                                           i+e+iGntPlvrLn l+e+ kaevlvk+es+nP ssvkdri++amie  e++g++k+++ ++e+tsGntGial
  NCBI__GCF_000191585.1:WP_013644774.1  15 ITETIGNTPLVRLNkLTEGSKAEVLVKVESFNPLSSVKDRIGVAMIEAGEEAGVIKENTILIEPTSGNTGIAL 87 
                                           689***********99********************************************************* PP

                             TIGR01139  73 amvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanp 145
                                           a+vaaa+gykliltmp+tms+errkll  +Gae+vLt+ga+gm ga++kaeel++e p   ++++qf+n anp
  NCBI__GCF_000191585.1:WP_013644774.1  88 AFVAAAKGYKLILTMPDTMSIERRKLLALLGAEIVLTPGANGMPGAVAKAEELAAEIP-GAVMPQQFKNIANP 159
                                           **********************************************************.556*********** PP

                             TIGR01139 146 eihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGig 218
                                           +ihr+tta+ei++d+dgk+d++v+g+GtGGtitGv+ +lke kp++k+vaveP++spvlsgg pgphkiqGig
  NCBI__GCF_000191585.1:WP_013644774.1 160 KIHRETTAQEIWRDTDGKVDVLVSGTGTGGTITGVATALKELKPEFKAVAVEPVTSPVLSGGSPGPHKIQGIG 232
                                           ************************************************************************* PP

                             TIGR01139 219 agfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtge 290
                                           +gfiP+vL++e+ide+++vsd++a +t  +la+eeGil+GissGaav+aal++akk e ++k+ivvilpdtge
  NCBI__GCF_000191585.1:WP_013644774.1 233 PGFIPDVLQTEIIDEIVQVSDDDAAQTLLKLAREEGILAGISSGAAVFAALQLAKKDEyAGKQIVVILPDTGE 305
                                           **********************************************************9************** PP

                             TIGR01139 291 rYlsta 296
                                           rYls++
  NCBI__GCF_000191585.1:WP_013644774.1 306 RYLSMD 311
                                           ****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (328 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: 23.76
//
[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