Alignments for a candidate for cysK in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Sphingomonas koreensis DSMZ 15582

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Ga0059261_3644 Ga0059261_3644 cysteine synthase A

Query= BRENDA::P37887
         (308 letters)



>FitnessBrowser__Korea:Ga0059261_3644
          Length = 306

 Score =  327 bits (837), Expect = 3e-94
 Identities = 168/300 (56%), Positives = 215/300 (71%), Gaps = 3/300 (1%)

Query: 5   ANSITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLKA 64
           AN+I E IGNTP +++ RL     A+V++K E  NPG S+KDRI L+M+EAAE +G LK 
Sbjct: 3   ANTILETIGNTPHIRIQRLFP--GAEVWVKSERSNPGGSIKDRIALSMVEAAEADGSLKP 60

Query: 65  GNTIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGMK 124
           G TI+EPTSGNTG+GLAMVAA KG K ILVMP++MS+ERR L+ AYGA   LTP  +GMK
Sbjct: 61  GGTIVEPTSGNTGVGLAMVAAVKGYKLILVMPESMSIERRRLMLAYGATFDLTPREKGMK 120

Query: 125 GAIKKAEELAEKH-GYFVPQQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTGGT 183
           GAI++A E+ E   G ++PQQF NP+N ++H +TT +EI+  F D  +D  + G+GTGG 
Sbjct: 121 GAIERAVEIVESTPGAWMPQQFENPANVDVHVKTTAQEILNDFADAPVDVIITGVGTGGH 180

Query: 184 ITGAGEVLKEAYPSIKIYAVEPSDSPVLSGGKPGPHKIQGIGAGFVPDILNTEVYDEIFP 243
           ITG  E LK+++P++K+YAVEP  SPV+SGG+PGPH IQGIGAGFVP  L+T+  D    
Sbjct: 181 ITGVAETLKKSWPNLKVYAVEPELSPVISGGQPGPHPIQGIGAGFVPKNLHTDAIDGAIQ 240

Query: 244 VKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSNGERYLSTP 303
           V    A +YARRAAREEG+L GISSGA + A  +    L  G +VL      GERYLS P
Sbjct: 241 VDAGNAKDYARRAAREEGLLVGISSGATLAAIAKKLPDLPAGSRVLGFNYDTGERYLSVP 300


Lambda     K      H
   0.313    0.134    0.373 

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: 280
Number of extensions: 10
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: 306
Length adjustment: 27
Effective length of query: 281
Effective length of database: 279
Effective search space:    78399
Effective search space used:    78399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate Ga0059261_3644 Ga0059261_3644 (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.11900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-120  388.4   0.0   1.2e-120  388.2   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3644  Ga0059261_3644 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3644  Ga0059261_3644 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.2   0.0  1.2e-120  1.2e-120       2     296 ..       7     300 ..       6     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 388.2 bits;  conditional E-value: 1.2e-120
                                 TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGi 70 
                                                e+iGntP +r+++  +  aev vk e  nP++s+kdrial+m+e ae +g lk+g tive+tsGntG+
  lcl|FitnessBrowser__Korea:Ga0059261_3644   7 LETIGNTPHIRIQRLFP-GAEVWVKSERSNPGGSIKDRIALSMVEAAEADGSLKPGGTIVEPTSGNTGV 74 
                                               689**********5555.8************************************************** PP

                                 TIGR01139  71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqf 139
                                               +lamvaa +gyklil+mpe+ms+err+l+ ayGa + Lt+ ++gmkgaie+a e+ve+tp ++ +++qf
  lcl|FitnessBrowser__Korea:Ga0059261_3644  75 GLAMVAAVKGYKLILVMPESMSIERRRLMLAYGATFDLTPREKGMKGAIERAVEIVESTPGAW-MPQQF 142
                                               ************************************************************999.***** PP

                                 TIGR01139 140 enpanpeihrkttapeilkdldgk.ldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsgg 207
                                               enpan ++h ktta+eil+d+ ++ +d++++gvGtGG itGv+e+lk++ p++kv+aveP+ spv+sgg
  lcl|FitnessBrowser__Korea:Ga0059261_3644 143 ENPANVDVHVKTTAQEILNDFADApVDVIITGVGTGGHITGVAETLKKSWPNLKVYAVEPELSPVISGG 211
                                               *********************9988******************************************** PP

                                 TIGR01139 208 kpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle 276
                                               +pgph iqGigagf+Pk+L ++ id  i+v+  +a ++arr a+eeG+lvGissGa++aa  k   +l 
  lcl|FitnessBrowser__Korea:Ga0059261_3644 212 QPGPHPIQGIGAGFVPKNLHTDAIDGAIQVDAGNAKDYARRAAREEGLLVGISSGATLAAIAKKLPDLP 280
                                               ***********************************************************9888888888 PP

                                 TIGR01139 277 kdkkivvilpdtgerYlsta 296
                                               ++ +++    dtgerYls++
  lcl|FitnessBrowser__Korea:Ga0059261_3644 281 AGSRVLGFNYDTGERYLSVP 300
                                               ******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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: 00:00:00.01
# Mc/sec: 7.20
//
[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