Aligments for a candidate for cysK in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Aligments for a candidate for cysK in Pseudomonas simiae WCS417

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1476 PS417_07505 cysteine synthase

Query= BRENDA::P0ABK5
         (323 letters)



>lcl|FitnessBrowser__WCS417:GFF1476 PS417_07505 cysteine synthase
          Length = 324

 Score =  442 bits (1138), Expect = e-129
 Identities = 229/324 (70%), Positives = 264/324 (81%), Gaps = 3/324 (0%)

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

Query: 59  LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118
           LKPG+ +VEPTSGNTGI LA+VAAARGYKL LTMP +MSIERRK+LKALGA LVLTE AK
Sbjct: 61  LKPGMTIVEPTSGNTGIGLAFVAAARGYKLLLTMPASMSIERRKVLKALGAELVLTEPAK 120

Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178
           GMKGAI+KA EIVAS+P  Y +  QF NPANP IHEKTTGPEIW DTDG VDV +AGVGT
Sbjct: 121 GMKGAIEKAGEIVASDPATYFMPAQFENPANPAIHEKTTGPEIWNDTDGAVDVLVAGVGT 180

Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238
           GGT+TGVSRYIK   GK  ++SVAVEP  SPVI QALAGEEIKP PHKIQGIGAGF+P N
Sbjct: 181 GGTITGVSRYIKNIAGK-PILSVAVEPIVSPVITQALAGEEIKPSPHKIQGIGAGFVPKN 239

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

Query: 299 LPSSGERYLSTALFADLFTEKELQ 322
           LP SGERYLS+ LF+DLFTE+E Q
Sbjct: 300 LPDSGERYLSSMLFSDLFTEQENQ 323


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: 405
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 GFF1476 PS417_07505 (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.28655.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-138  445.4   0.8   5.4e-138  445.2   0.8    1.0  1  lcl|FitnessBrowser__WCS417:GFF1476  PS417_07505 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1476  PS417_07505 cysteine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.2   0.8  5.4e-138  5.4e-138       3     298 .]      10     313 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 445.2 bits;  conditional E-value: 5.4e-138
                           TIGR01139   3 eliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaa 77 
                                         + iGntPlv++n++++  + +l+k+e +nP++svk+ri+++mi+dae +g+lk+g tive+tsGntGi+la+vaa
  lcl|FitnessBrowser__WCS417:GFF1476  10 HSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGMTIVEPTSGNTGIGLAFVAA 84 
                                         78************************************************************************* PP

                           TIGR01139  78 argykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrktt 152
                                         argykl+ltmp++ms+errk+lka+GaelvLt++a+gmkgaieka e+v+++p +y+++ qfenpanp+ih+ktt
  lcl|FitnessBrowser__WCS417:GFF1476  85 ARGYKLLLTMPASMSIERRKVLKALGAELVLTEPAKGMKGAIEKAGEIVASDPATYFMPAQFENPANPAIHEKTT 159
                                         *************************************************************************** PP

                           TIGR01139 153 apeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigag 220
                                         +pei++d+dg++d++vagvGtGGtitGv++++k+  +  i +vaveP  spv++++      kp phkiqGigag
  lcl|FitnessBrowser__WCS417:GFF1476 160 GPEIWNDTDGAVDVLVAGVGTGGTITGVSRYIKNIAGkPILSVAVEPIVSPVITQAlageeiKPSPHKIQGIGAG 234
                                         **********************************99868****************9999999************* PP

                           TIGR01139 221 fiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYls 294
                                         f+Pk+Ld +++d+v  v+d+e+ ++a rl++eeGil Gis Gaa+a a+++a+k+e ++k+ivvilpd+gerYls
  lcl|FitnessBrowser__WCS417:GFF1476 235 FVPKNLDLSMVDRVELVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEmQGKTIVVILPDSGERYLS 309
                                         ********************************************************9****************** PP

                           TIGR01139 295 taLf 298
                                           Lf
  lcl|FitnessBrowser__WCS417:GFF1476 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.72
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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