Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N1B4

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Pf1N1B4_3374 Cysteine synthase (EC 2.5.1.47)

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374
          Length = 324

 Score =  444 bits (1141), Expect = e-129
 Identities = 226/325 (69%), Positives = 268/325 (82%), Gaps = 3/325 (0%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIG--NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGV 58
           MS+I+ DN+ +IG+TPLV++NRI      ILAK+E RNP +SVKCRIGANMIWDAE  G 
Sbjct: 1   MSRIYADNAHSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGK 60

Query: 59  LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118
           LKPG+ ++EPTSGNTGI LA+VAAARGY+L LTMP +MSIERRK+LKALGA LVLTE AK
Sbjct: 61  LKPGMTIIEPTSGNTGIGLAFVAAARGYRLVLTMPASMSIERRKVLKALGAELVLTEPAK 120

Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178
           GMKGAI+KA EI+AS+P  Y +  QF NPANP IHEKTTGPEIW DTDG VDV +AGVGT
Sbjct: 121 GMKGAIEKAAEILASDPSTYFMPGQFENPANPAIHEKTTGPEIWSDTDGAVDVLVAGVGT 180

Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238
           GGT+TGVSRYIK T+GK  +ISVAVEP  SPVI QA+AGEEIKP PHKIQGIGAGF+P N
Sbjct: 181 GGTITGVSRYIKNTQGK-PIISVAVEPVVSPVITQAMAGEEIKPSPHKIQGIGAGFVPKN 239

Query: 239 LDLKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVI 298
           LDL +VD+V  ++++E+ + A RLM+EEGIL+GIS GAA+A A++L E      K IVVI
Sbjct: 240 LDLSMVDRVELVSDDESKAMALRLMQEEGILSGISCGAAMAVAVRLAETPEMQGKTIVVI 299

Query: 299 LPSSGERYLSTALFADLFTEKELQQ 323
           LP SGERYLS+ LF+DLFTE+E QQ
Sbjct: 300 LPDSGERYLSSMLFSDLFTEQENQQ 324


Lambda     K      H
   0.313    0.133    0.368 

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: 398
Number of extensions: 17
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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 Pf1N1B4_3374 (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.28641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.6e-138  446.9   0.9   1.9e-138  446.7   0.9    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374  Cysteine synthase (EC 2.5.1.47)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374  Cysteine synthase (EC 2.5.1.47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.7   0.9  1.9e-138  1.9e-138       3     298 .]      10     313 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.7 bits;  conditional E-value: 1.9e-138
                                      TIGR01139   3 eliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsG 66 
                                                    + iGntPlv++n++++  + +l+k+e +nP++svk+ri+++mi+dae +g+lk+g ti+e+tsG
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374  10 HSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGMTIIEPTSG 73 
                                                    78************************************************************** PP

                                      TIGR01139  67 ntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetp 130
                                                    ntGi+la+vaaargy+l+ltmp++ms+errk+lka+GaelvLt++a+gmkgaieka e+++++p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374  74 NTGIGLAFVAAARGYRLVLTMPASMSIERRKVLKALGAELVLTEPAKGMKGAIEKAAEILASDP 137
                                                    **************************************************************** PP

                                      TIGR01139 131 nkylllkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikv 193
                                                    ++y+++ qfenpanp+ih+ktt+pei+ d+dg++d++vagvGtGGtitGv++++k++++  i +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374 138 STYFMPGQFENPANPAIHEKTTGPEIWSDTDGAVDVLVAGVGTGGTITGVSRYIKNTQGkPIIS 201
                                                    ********************************************************99978*** PP

                                      TIGR01139 194 vavePaespvlsgg......kpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlak 251
                                                    vaveP+ spv++++      kp phkiqGigagf+Pk+Ld +++d+v  vsd+e+ ++a rl++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374 202 VAVEPVVSPVITQAmageeiKPSPHKIQGIGAGFVPKNLDLSMVDRVELVSDDESKAMALRLMQ 265
                                                    *************9999999******************************************** PP

                                      TIGR01139 252 eeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298
                                                    eeGil+Gis Gaa+a a+++a+ +e ++k+ivvilpd+gerYls  Lf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374 266 EEGILSGISCGAAMAVAVRLAETPEmQGKTIVVILPDSGERYLSSMLF 313
                                                    *************************9*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (324 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: 00:00:00.01
# Mc/sec: 7.37
//
[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