Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

Align cysteine synthase (EC 2.5.1.47); L-3-cyanoalanine synthase (EC 4.4.1.9) (characterized)
to candidate Ac3H11_1975 Cysteine synthase (EC 2.5.1.47)

Query= BRENDA::Q84IF9
         (308 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1975
          Length = 305

 Score =  324 bits (831), Expect = 1e-93
 Identities = 168/297 (56%), Positives = 217/297 (73%), Gaps = 2/297 (0%)

Query: 5   VNSITELIGDTPAVKLNRIVDEDSADVYLKLEFMNPGSSVKDRIALAMIEAAEKAGKLKP 64
           V++I + IG+TP V++NR+     A+V++K E  NPG S+KDRIAL+M+E AEK+G L+P
Sbjct: 3   VDNILQTIGNTPHVRINRLFGP-GANVWVKSERSNPGGSIKDRIALSMVEDAEKSGALQP 61

Query: 65  GDTIVEPTSGNTGIGLAMVAAAKGYKAVLVMPDTMSLERRNLLRAYGAELVLTPGAQGMR 124
           G TI+EPTSGNTGIGLA+VAA KGYK +LVMPD+MS+ERR L+ AYGA+  LTP  +GM+
Sbjct: 62  GGTIIEPTSGNTGIGLALVAAVKGYKLILVMPDSMSIERRRLMLAYGAQFDLTPREKGMK 121

Query: 125 GPIAKAEEL-VREHGYFMPQQFKNEANPEIHRLTTGKEIVEQMGDQLDAFVAGVGTGGTT 183
           G IA+A+EL  +  G ++PQQF+N AN ++H  TT +EI+    + +D  + GVGTGG  
Sbjct: 122 GAIARAQELQAQTPGSWIPQQFENPANIDVHVRTTAQEILADFPEGIDVLITGVGTGGHI 181

Query: 184 TGAGKVLREAYPNIKIYAVEPADSPVLSGGKPGPHKIQGIGAGFVPDILDTSIYDGVITV 243
           TG  KVL+  +P +K++AVEP  SPV+SGG+P PH IQGIGAGF+P  LDTS+ DGVI V
Sbjct: 182 TGVAKVLKAKFPQLKVFAVEPTASPVISGGQPSPHPIQGIGAGFIPKNLDTSLLDGVIQV 241

Query: 244 TTEEAFAAARRAAREEGILGGISSGAAIHAALKVAKELGKGKKVLAIIPSNGERYLS 300
             E A   ARRAAREEG+L GISSGA + A  +   EL  G KVL      GERYLS
Sbjct: 242 DAEPAREFARRAAREEGLLVGISSGATLAAIAQKLPELPAGAKVLGFNYDTGERYLS 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: 270
Number of extensions: 8
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: 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 Ac3H11_1975 (Cysteine synthase (EC 2.5.1.47))
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.19227.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.3e-124  399.9   0.0   3.8e-124  399.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975  Cysteine synthase (EC 2.5.1.47)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975  Cysteine synthase (EC 2.5.1.47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.8   0.0  3.8e-124  3.8e-124       2     296 ..       7     300 ..       6     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 399.8 bits;  conditional E-value: 3.8e-124
                                        TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktivea 63 
                                                       ++iGntP vr+n+  +  a+v vk e  nP++s+kdrial+m+edaek+g l++g ti+e+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975   7 LQTIGNTPHVRINRLFGPGANVWVKSERSNPGGSIKDRIALSMVEDAEKSGALQPGGTIIEP 68 
                                                      589**********99*********************************************** PP

                                        TIGR01139  64 tsGntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeel 125
                                                      tsGntGi+la+vaa +gyklil+mp++ms+err+l+ ayGa++ Lt+ ++gmkgai++a+el
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975  69 TSGNTGIGLALVAAVKGYKLILVMPDSMSIERRRLMLAYGAQFDLTPREKGMKGAIARAQEL 130
                                                      ************************************************************** PP

                                        TIGR01139 126 veetpnkylllkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkek 187
                                                       ++tp ++ +++qfenpan ++h +tta+eil d+ + +d++++gvGtGG itGv++vlk k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975 131 QAQTPGSW-IPQQFENPANIDVHVRTTAQEILADFPEGIDVLITGVGTGGHITGVAKVLKAK 191
                                                      *******9.***************************************************** PP

                                        TIGR01139 188 kpdikvvavePaespvlsggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrl 249
                                                      +p++kv+aveP++spv+sgg+p ph iqGigagfiPk+Ld++++d vi+v+ e a e arr 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975 192 FPQLKVFAVEPTASPVISGGQPSPHPIQGIGAGFIPKNLDTSLLDGVIQVDAEPAREFARRA 253
                                                      ************************************************************** PP

                                        TIGR01139 250 akeeGilvGissGaavaaalkvakklekdkkivvilpdtgerYlsta 296
                                                      a+eeG+lvGissGa++aa  +   +l +++k++    dtgerYls++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1975 254 AREEGLLVGISSGATLAAIAQKLPELPAGAKVLGFNYDTGERYLSVE 300
                                                      ****************99877777777******************97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.15
//
[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