Alignments for a candidate for cysK in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pseudomonas stutzeri RCH2

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1816 Psest_1855 cysteine synthase A

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__psRCH2:GFF1816
          Length = 324

 Score =  452 bits (1164), Expect = e-132
 Identities = 229/325 (70%), Positives = 269/325 (82%), Gaps = 3/325 (0%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIG--NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGV 58
           MS+IF DN+ +IG+TPLV +NR+G     I+AK+E RNP++SVKCRIGA MIWDAE  G 
Sbjct: 1   MSRIFADNARSIGNTPLVMINRLGPKGVTIMAKIEGRNPAYSVKCRIGAGMIWDAEDSGR 60

Query: 59  LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118
           +KPG+ LVEPTSGNTGI LA+VAAARGYKL LTMP +MS+ERRK+LKALGA LVLTE AK
Sbjct: 61  IKPGMTLVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSLERRKVLKALGAELVLTEPAK 120

Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178
           GMKGAI+KA EI ASNPE+Y + QQF NP+NP IHEKTTGPEIW DTDG +DV +AGVGT
Sbjct: 121 GMKGAIEKAAEIAASNPEQYYMPQQFENPSNPAIHEKTTGPEIWNDTDGSIDVLVAGVGT 180

Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238
           GGT+TGVSRYIK TKGK  +ISVAVEPT SPVI+Q LAG+E+KP PHKIQGIGAGF+P N
Sbjct: 181 GGTITGVSRYIKNTKGK-QIISVAVEPTSSPVISQTLAGDEVKPSPHKIQGIGAGFVPKN 239

Query: 239 LDLKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVI 298
           LDL +VD+V  + +EEA   A RLM EEGIL GIS GAA+AAA++L E      KNIVVI
Sbjct: 240 LDLSMVDRVELVDDEEAKQMALRLMREEGILCGISCGAAMAAAVRLAERPEMQGKNIVVI 299

Query: 299 LPSSGERYLSTALFADLFTEKELQQ 323
           LP SGERYLS+ LF+D+F+E+EL Q
Sbjct: 300 LPDSGERYLSSMLFSDMFSEQELVQ 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: 401
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 GFF1816 Psest_1855 (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.9223.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.1e-141  454.7   0.4   8.1e-141  454.5   0.4    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1816  Psest_1855 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1816  Psest_1855 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.5   0.4  8.1e-141  8.1e-141       2     298 .]       9     313 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 454.5 bits;  conditional E-value: 8.1e-141
                           TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamva 76 
                                         ++ iGntPlv +n+  ++ + +++k+e +nP++svk+ri++ mi+dae++g +k+g t+ve+tsGntGi+la+va
  lcl|FitnessBrowser__psRCH2:GFF1816   9 ARSIGNTPLVMINRLGPKGVTIMAKIEGRNPAYSVKCRIGAGMIWDAEDSGRIKPGMTLVEPTSGNTGIGLAFVA 83 
                                         578**********99999********************************************************* PP

                           TIGR01139  77 aargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkt 151
                                         aargykl+ltmp++mslerrk+lka+GaelvLt++a+gmkgaieka e+++++p++y++++qfenp+np+ih+kt
  lcl|FitnessBrowser__psRCH2:GFF1816  84 AARGYKLMLTMPASMSLERRKVLKALGAELVLTEPAKGMKGAIEKAAEIAASNPEQYYMPQQFENPSNPAIHEKT 158
                                         *************************************************************************** PP

                           TIGR01139 152 tapeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGiga 219
                                         t+pei++d+dg++d++vagvGtGGtitGv++++k++k+ +i +vaveP++spv+s++      kp phkiqGiga
  lcl|FitnessBrowser__psRCH2:GFF1816 159 TGPEIWNDTDGSIDVLVAGVGTGGTITGVSRYIKNTKGkQIISVAVEPTSSPVISQTlagdevKPSPHKIQGIGA 233
                                         ************************************9989****************999**************** PP

                           TIGR01139 220 gfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYl 293
                                         gf+Pk+Ld +++d+v  v+deea ++a rl++eeGil Gis Gaa+aaa+++a+++e ++k+ivvilpd+gerYl
  lcl|FitnessBrowser__psRCH2:GFF1816 234 GFVPKNLDLSMVDRVELVDDEEAKQMALRLMREEGILCGISCGAAMAAAVRLAERPEmQGKNIVVILPDSGERYL 308
                                         *********************************************************9***************** PP

                           TIGR01139 294 staLf 298
                                         s  Lf
  lcl|FitnessBrowser__psRCH2:GFF1816 309 SSMLF 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: 9.09
//
[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