Alignments for a candidate for cysK in Caldicellulosiruptor kronotskyensis 2002

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Caldicellulosiruptor kronotskyensis 2002

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_013430091.1 CALKRO_RS05590 cysteine synthase A

Query= BRENDA::P9WP55
         (310 letters)



>NCBI__GCF_000166775.1:WP_013430091.1
          Length = 308

 Score =  385 bits (989), Expect = e-112
 Identities = 194/303 (64%), Positives = 240/303 (79%)

Query: 3   IAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIK 62
           I   I +LIG+TPLVRL +++    A+IVAK+E+FNP  SVKDRIG+AM++ AE+ GLI 
Sbjct: 2   IYNSIVELIGKTPLVRLNKLSKDLDAEIVAKIEYFNPGGSVKDRIGLAMIEDAEKRGLIN 61

Query: 63  PDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGM 122
            +T+I+EPTSGNTGIALAMVCA +GY+ +LTMPETMS+ERR LLRAYGA+++LTPG  GM
Sbjct: 62  KETVIVEPTSGNTGIALAMVCAVKGYKLILTMPETMSIERRKLLRAYGAQIVLTPGEKGM 121

Query: 123 SGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGT 182
            GAI KA E+  +    F+PQQFEN +NP IHR TTA E+W DT+GK+DI VAGVGTGGT
Sbjct: 122 KGAIEKAFEIYNSTPNAFMPQQFENLSNPEIHRKTTALEIWNDTNGKIDIFVAGVGTGGT 181

Query: 183 ITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIIT 242
           ITGV +V+KE+KPS + VAVEP  S VLSG +  PH IQGIGAGFVP VL+  + D+I+ 
Sbjct: 182 ITGVGEVLKEKKPSVKVVAVEPYDSAVLSGEKPRPHKIQGIGAGFVPKVLNTKIYDQIVK 241

Query: 243 VGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLST 302
           V  EDA  ++R LAREEG+LVGISSGAA   AL+VA++ EN  K+IVV+LPD GERYLST
Sbjct: 242 VKVEDAYEMSRYLAREEGILVGISSGAALYGALEVAKKQENKKKMIVVLLPDTGERYLST 301

Query: 303 PLF 305
            LF
Sbjct: 302 DLF 304


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: 296
Number of extensions: 6
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: 308
Length adjustment: 27
Effective length of query: 283
Effective length of database: 281
Effective search space:    79523
Effective search space used:    79523
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_013430091.1 CALKRO_RS05590 (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.2052411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-151  490.3   1.3   1.2e-151  490.1   1.3    1.0  1  NCBI__GCF_000166775.1:WP_013430091.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430091.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.1   1.3  1.2e-151  1.2e-151       2     298 .]       7     304 ..       6     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 490.1 bits;  conditional E-value: 1.2e-151
                             TIGR01139   2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGiala 73 
                                            eliG+tPlvrLn l ++ +ae+++k+e++nP++svkdri+lamiedaek+gl++k+++ive+tsGntGiala
  NCBI__GCF_000166775.1:WP_013430091.1   7 VELIGKTPLVRLNkLSKDLDAEIVAKIEYFNPGGSVKDRIGLAMIEDAEKRGLINKETVIVEPTSGNTGIALA 79 
                                           689**********9999******************************************************** PP

                             TIGR01139  74 mvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpe 146
                                           mv+a +gykliltmpetms+errkll+ayGa++vLt+g++gmkgaieka e+ ++tpn++ +++qfen +npe
  NCBI__GCF_000166775.1:WP_013430091.1  80 MVCAVKGYKLILTMPETMSIERRKLLRAYGAQIVLTPGEKGMKGAIEKAFEIYNSTPNAF-MPQQFENLSNPE 151
                                           *********************************************************999.************ PP

                             TIGR01139 147 ihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGiga 219
                                           ihrktta ei++d++gk+d+fvagvGtGGtitGvgevlkekkp++kvvaveP +s+vlsg+kp phkiqGiga
  NCBI__GCF_000166775.1:WP_013430091.1 152 IHRKTTALEIWNDTNGKIDIFVAGVGTGGTITGVGEVLKEKKPSVKVVAVEPYDSAVLSGEKPRPHKIQGIGA 224
                                           ************************************************************************* PP

                             TIGR01139 220 gfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtger 291
                                           gf+PkvL+++++d+++kv+ e+a+e++r la+eeGilvGissGaa++ al+vakk+e k k+ivv+lpdtger
  NCBI__GCF_000166775.1:WP_013430091.1 225 GFVPKVLNTKIYDQIVKVKVEDAYEMSRYLAREEGILVGISSGAALYGALEVAKKQEnKKKMIVVLLPDTGER 297
                                           *******************************************************9989999*********** PP

                             TIGR01139 292 YlstaLf 298
                                           Ylst+Lf
  NCBI__GCF_000166775.1:WP_013430091.1 298 YLSTDLF 304
                                           ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (308 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: 26.38
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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