Alignments for a candidate for cysK in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Saccharomonospora cyanea NA-134

Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_005458675.1 SACCYDRAFT_RS19045 cysteine synthase

Query= metacyc::MONOMER-20568
         (299 letters)



>NCBI__GCF_000244975.1:WP_005458675.1
          Length = 316

 Score =  243 bits (619), Expect = 5e-69
 Identities = 128/295 (43%), Positives = 192/295 (65%), Gaps = 6/295 (2%)

Query: 3   YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62
           Y ++L+ +G TPLV +  L+P+P+V+++AKLE  NPTGS+KDR AL MIE AE +G L  
Sbjct: 4   YASLLDALGGTPLVGLPRLSPSPEVRLWAKLEDRNPTGSIKDRPALAMIEAAERDGILKS 63

Query: 63  GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTD 122
           G TI+E TSGNTGI LAM  ++KGY ++ VM E  S ERR++++A+GA I+ +    G++
Sbjct: 64  GDTILEPTSGNTGISLAMAAKLKGYGMVCVMPENTSEERRQLLQAYGARIVYSPAAGGSN 123

Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGT 182
            A+R+  EL K NP  +    Q+ N  N  AHY  T  E+  +   T+THFV  +GT+GT
Sbjct: 124 EAVRRAKELAKANP-DWVMLYQYGNPANADAHYYGTGPEL-LKDLPTLTHFVGGLGTTGT 181

Query: 183 LMGVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAF 242
           L+GVG+ LRE  P++++I A+P  G  + GL++++E  VP +Y  + +     + + +A 
Sbjct: 182 LVGVGRYLREHKPDVQVIAAEPRYGELVYGLRNLDEGFVPELYDPEVLSGRYSVGAYDAL 241

Query: 243 AKAREIVAQEGIFIGMSSGAAMLAAQKLAEKI----DSGVIVVLFADRGEKYLST 293
            + RE++ +EGIF G+S+GA + AA  +A K+     S  I  + AD G KYLST
Sbjct: 242 RRTRELLEKEGIFAGISTGAVLHAALGVANKVLKKGGSADIAFVVADAGWKYLST 296


Lambda     K      H
   0.315    0.133    0.367 

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: 294
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: 299
Length of database: 316
Length adjustment: 27
Effective length of query: 272
Effective length of database: 289
Effective search space:    78608
Effective search space used:    78608
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_005458675.1 SACCYDRAFT_RS19045 (cysteine synthase)
to HMM TIGR01136 (cysteine synthase (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/TIGR01136.hmm
# target sequence database:        /tmp/gapView.2946509.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01136  [M=299]
Accession:   TIGR01136
Description: cysKM: cysteine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-109  352.3   0.0   1.4e-109  352.1   0.0    1.0  1  NCBI__GCF_000244975.1:WP_005458675.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244975.1:WP_005458675.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.1   0.0  1.4e-109  1.4e-109       3     299 .]       9     299 ..       7     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.1 bits;  conditional E-value: 1.4e-109
                             TIGR01136   3 eliGntPlvrln.lseelkaevlvKlEsrnPsgSvKdRialsmildAekrgllkkgktiieatSGNtGiaLAm 74 
                                           +++G tPlv l  ls++ ++++++KlE+rnP+gS+KdR+al+mi+ Ae++g lk g+ti+e+tSGNtGi+LAm
  NCBI__GCF_000244975.1:WP_005458675.1   9 DALGGTPLVGLPrLSPSPEVRLWAKLEDRNPTGSIKDRPALAMIEAAERDGILKSGDTILEPTSGNTGISLAM 81 
                                           789*********9************************************************************ PP

                             TIGR01136  75 vaaakgyklilvmpetmslERrkllkayGaelvlteaeegmkgaiekakelaeeepekyvllkqfeNpaNpea 147
                                           +a  kgy +++vmpe++s+ERr+ll+ayGa++v ++a+ g++ a+++akela+++p  +v+l q+ NpaN +a
  NCBI__GCF_000244975.1:WP_005458675.1  82 AAKLKGYGMVCVMPENTSEERRQLLQAYGARIVYSPAAGGSNEAVRRAKELAKANP-DWVMLYQYGNPANADA 153
                                           ******************************************************98.899************* PP

                             TIGR01136 148 HrkttgpEilkdtdgkidafvagvGtgGtitGvgrvlkekkpnvkivavePaespvlsegkpgphkiqgigag 220
                                           H+  tgpE+lkd+  ++++fv g+Gt+Gt++Gvgr+l+e+kp+v+++a+eP+++++ ++g      ++++++g
  NCBI__GCF_000244975.1:WP_005458675.1 154 HYYGTGPELLKDLP-TLTHFVGGLGTTGTLVGVGRYLREHKPDVQVIAAEPRYGEL-VYG------LRNLDEG 218
                                           *************9.9***************************************9.677......9****** PP

                             TIGR01136 221 fiPkildeelldevikvededaietarrlakeegilvGiSsGaavaaalkvakklek..edkkivvilpdage 291
                                           f+P+++d e+l   ++v + da++ +r+l ++egi++GiS+Ga+++aal va+k  k   +++i  +++dag+
  NCBI__GCF_000244975.1:WP_005458675.1 219 FVPELYDPEVLSGRYSVGAYDALRRTRELLEKEGIFAGISTGAVLHAALGVANKVLKkgGSADIAFVVADAGW 291
                                           *****************************************************9887345689********** PP

                             TIGR01136 292 rYLstelf 299
                                           +YLst  +
  NCBI__GCF_000244975.1:WP_005458675.1 292 KYLSTGAY 299
                                           *****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (316 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: 19.58
//
[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