Alignments for a candidate for cysK in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Cupriavidus basilensis 4G11

Align cysteine synthase (EC 2.5.1.47); L-3-cyanoalanine synthase (EC 4.4.1.9) (characterized)
to candidate RR42_RS21960 RR42_RS21960 cysteine synthase

Query= BRENDA::Q84IF9
         (308 letters)



>FitnessBrowser__Cup4G11:RR42_RS21960
          Length = 305

 Score =  318 bits (816), Expect = 8e-92
 Identities = 170/296 (57%), Positives = 212/296 (71%), Gaps = 2/296 (0%)

Query: 6   NSITELIGDTPAVKLNRIVDEDSADVYLKLEFMNPGSSVKDRIALAMIEAAEKAGKLKPG 65
           ++I + IG+TP +++ R+   D+  V++K E  NPG S+KDRIAL+M+EAAE++G LKPG
Sbjct: 4   DNILQTIGNTPHIRVQRLFG-DTHQVWIKSERANPGGSIKDRIALSMVEAAEQSGVLKPG 62

Query: 66  DTIVEPTSGNTGIGLAMVAAAKGYKAVLVMPDTMSLERRNLLRAYGAELVLTPGAQGMRG 125
            TI+EPTSGNTGIGLAMVAA KGYK VLVMPD+MS+ERR L+ AYGA   LTP  +GM+G
Sbjct: 63  GTIIEPTSGNTGIGLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTPREKGMKG 122

Query: 126 PIAKAEELVREH-GYFMPQQFKNEANPEIHRLTTGKEIVEQMGDQLDAFVAGVGTGGTTT 184
            IA+AEELV    G +MPQQF+N AN E H  TT  EI+      +DA V GVGTGG  T
Sbjct: 123 AIARAEELVAATPGAWMPQQFENPANIEAHVNTTALEILADFPQGIDALVTGVGTGGHIT 182

Query: 185 GAGKVLREAYPNIKIYAVEPADSPVLSGGKPGPHKIQGIGAGFVPDILDTSIYDGVITVT 244
           G  +VL++ +P +K+YAVEP  SPV+SGG P PH IQGIGAGF+P  LDT++ DGVI V 
Sbjct: 183 GCARVLKQKWPALKVYAVEPVASPVISGGAPAPHPIQGIGAGFIPRNLDTALLDGVIQVD 242

Query: 245 TEEAFAAARRAAREEGILGGISSGAAIHAALKVAKELGKGKKVLAIIPSNGERYLS 300
            E A   ARRAAREEG+L GISSGA + A  +   +L  G  VL      GERYL+
Sbjct: 243 AEPAREMARRAAREEGMLVGISSGATLAAIAQKLPDLPAGATVLGFNYDTGERYLT 298


Lambda     K      H
   0.314    0.134    0.374 

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: 271
Number of extensions: 7
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: 308
Length of database: 305
Length adjustment: 27
Effective length of query: 281
Effective length of database: 278
Effective search space:    78118
Effective search space used:    78118
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS21960 RR42_RS21960 (cysteine synthase)
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.9268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-122  392.0   0.0   9.6e-122  391.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21960  RR42_RS21960 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21960  RR42_RS21960 cysteine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.9   0.0  9.6e-122  9.6e-122       2     296 ..       7     300 ..       6     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 391.9 bits;  conditional E-value: 9.6e-122
                                 TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGi 70 
                                                ++iGntP +r+++  + + +v +k e  nP++s+kdrial+m+e ae++g+lk+g ti+e+tsGntGi
  lcl|FitnessBrowser__Cup4G11:RR42_RS21960   7 LQTIGNTPHIRVQRLFGDTHQVWIKSERANPGGSIKDRIALSMVEAAEQSGVLKPGGTIIEPTSGNTGI 75 
                                               589****************************************************************** PP

                                 TIGR01139  71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqf 139
                                               +lamvaa +gykl+l+mp++ms+err+l+ ayGa + Lt+ ++gmkgai++aeelv++tp ++ +++qf
  lcl|FitnessBrowser__Cup4G11:RR42_RS21960  76 GLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTPREKGMKGAIARAEELVAATPGAW-MPQQF 143
                                               ************************************************************999.***** PP

                                 TIGR01139 140 enpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggk 208
                                               enpan e+h +tta eil d+ + +da+v+gvGtGG itG ++vlk+k p +kv+aveP++spv+sgg 
  lcl|FitnessBrowser__Cup4G11:RR42_RS21960 144 ENPANIEAHVNTTALEILADFPQGIDALVTGVGTGGHITGCARVLKQKWPALKVYAVEPVASPVISGGA 212
                                               ********************************************************************* PP

                                 TIGR01139 209 pgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakklek 277
                                               p ph iqGigagfiP++Ld+ ++d vi+v+ e a e+arr a+eeG+lvGissGa++aa  +   +l +
  lcl|FitnessBrowser__Cup4G11:RR42_RS21960 213 PAPHPIQGIGAGFIPRNLDTALLDGVIQVDAEPAREMARRAAREEGMLVGISSGATLAAIAQKLPDLPA 281
                                               *********************************************************99888888888* PP

                                 TIGR01139 278 dkkivvilpdtgerYlsta 296
                                               +++++    dtgerYl+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS21960 282 GATVLGFNYDTGERYLTVE 300
                                               ****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.37
//
[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