GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas putida KT2440

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate PP_4571 PP_4571 cysteine synthase A

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__Putida:PP_4571
          Length = 324

 Score =  447 bits (1151), Expect = e-130
 Identities = 226/325 (69%), Positives = 270/325 (83%), Gaps = 3/325 (0%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIG--NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGV 58
           MS+IF DN+ +IG+TPLV++NRI      ILAK+E RNP +SVKCRIGANM+WDAE  G 
Sbjct: 1   MSRIFADNAHSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMVWDAESSGK 60

Query: 59  LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118
           LKPG+ +VEPTSGNTGI LA+VAAARGYKL LTMP +MS+ERRK+LKALGA LVLT+ AK
Sbjct: 61  LKPGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSLERRKVLKALGAELVLTDPAK 120

Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178
           GMKGAI+KA EIVAS+PE+Y L  QF NPANP IHEKTTGPEIW DTDG +DV +AGVGT
Sbjct: 121 GMKGAIEKANEIVASDPEQYFLPGQFENPANPAIHEKTTGPEIWNDTDGAIDVLVAGVGT 180

Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238
           GGT+TGVSRYIK T+GK  ++SVAVEP  SP+I+Q LAGEE+KP PHKIQGIGAGF+P N
Sbjct: 181 GGTITGVSRYIKHTQGKA-ILSVAVEPVASPLISQTLAGEELKPSPHKIQGIGAGFVPKN 239

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

Query: 299 LPSSGERYLSTALFADLFTEKELQQ 323
           LP SGERYLS+ LF+D+F+E+E QQ
Sbjct: 300 LPDSGERYLSSMLFSDMFSEQETQQ 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: 407
Number of extensions: 18
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 PP_4571 PP_4571 (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.15019.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-141  456.9   0.6   1.7e-141  456.7   0.6    1.0  1  lcl|FitnessBrowser__Putida:PP_4571  PP_4571 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4571  PP_4571 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.6  1.7e-141  1.7e-141       3     298 .]      10     313 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 1.7e-141
                           TIGR01139   3 eliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaa 77 
                                         + iGntPlv++n++++  + +l+k+e +nP++svk+ri+++m++dae +g+lk+g tive+tsGntGi+la+vaa
  lcl|FitnessBrowser__Putida:PP_4571  10 HSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMVWDAESSGKLKPGMTIVEPTSGNTGIGLAFVAA 84 
                                         78************************************************************************* PP

                           TIGR01139  78 argykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrktt 152
                                         argykl+ltmp++mslerrk+lka+GaelvLtd+a+gmkgaieka+e+v+++p++y+l+ qfenpanp+ih+ktt
  lcl|FitnessBrowser__Putida:PP_4571  85 ARGYKLMLTMPASMSLERRKVLKALGAELVLTDPAKGMKGAIEKANEIVASDPEQYFLPGQFENPANPAIHEKTT 159
                                         *************************************************************************** PP

                           TIGR01139 153 apeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigag 220
                                         +pei++d+dg++d++vagvGtGGtitGv++++k++++  i +vaveP++sp++s++      kp phkiqGigag
  lcl|FitnessBrowser__Putida:PP_4571 160 GPEIWNDTDGAIDVLVAGVGTGGTITGVSRYIKHTQGkAILSVAVEPVASPLISQTlageelKPSPHKIQGIGAG 234
                                         **********************************9997899**************999***************** PP

                           TIGR01139 221 fiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYls 294
                                         f+Pk+Ld +++d+v +v+dee+ ++a rl++eeGil Gis Gaa+aaa+++a+k+e ++k+ivvilpd+gerYls
  lcl|FitnessBrowser__Putida:PP_4571 235 FVPKNLDLSIVDQVETVTDEESKAMAIRLMQEEGILCGISCGAAMAAAVRLAEKPEmQGKTIVVILPDSGERYLS 309
                                         ********************************************************9****************** PP

                           TIGR01139 295 taLf 298
                                           Lf
  lcl|FitnessBrowser__Putida:PP_4571 310 SMLF 313
                                         *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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.87
//
[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:

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:

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:

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:

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