Alignments for a candidate for cysK in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Dechlorosoma suillum PS

Align Cysteine synthase; CSase; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase; EC 2.5.1.47 (characterized)
to candidate Dsui_2521 Dsui_2521 cysteine synthase A

Query= SwissProt::Q59966
         (329 letters)



>FitnessBrowser__PS:Dsui_2521
          Length = 328

 Score =  520 bits (1338), Expect = e-152
 Identities = 257/328 (78%), Positives = 293/328 (89%)

Query: 1   MSTSGTFFADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAE 60
           M +   +F+DNS++IG+TPLVRLNR+  GAPATVLAKIEGRNPAYSVKCRIGAAM+WDAE
Sbjct: 1   MKSMSNWFSDNSRSIGRTPLVRLNRVTDGAPATVLAKIEGRNPAYSVKCRIGAAMVWDAE 60

Query: 61  QRGLLGPGKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLT 120
            RGLLGPGKEL+EPTSGNTGIALAFVAA  GIPLTLTMPETMSLERRKLLAAYGAKLVLT
Sbjct: 61  IRGLLGPGKELVEPTSGNTGIALAFVAAVYGIPLTLTMPETMSLERRKLLAAYGAKLVLT 120

Query: 121 EGVKGMTGAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVS 180
           EG KGM GA+ +AE+IAASDP +YVLLQQF+NPANPAIHE TTGPEIW DT   +DI VS
Sbjct: 121 EGTKGMGGAIAKAEEIAASDPGKYVLLQQFKNPANPAIHESTTGPEIWIDTDDKVDIFVS 180

Query: 181 GVGTGGTITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFI 240
           GVGTGGTITGVSRY K+T+G  + SVAVEP ASPV++Q R+G P+KPGPHKIQGIGAGF+
Sbjct: 181 GVGTGGTITGVSRYFKKTRGAKLWSVAVEPSASPVLTQTRNGEPVKPGPHKIQGIGAGFV 240

Query: 241 PENLDLSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTI 300
           P+ LDLSL+D +E+VSNEEA+AYARRLA+EEG+ISGIS GAAVA A RLAQ+ E+AGKTI
Sbjct: 241 PQVLDLSLIDAIEQVSNEEAVAYARRLAREEGIISGISSGAAVAVASRLAQRRENAGKTI 300

Query: 301 VVVLPDSGERYLSTALFDGIFNEQGLAV 328
           VV+LPDSGERYLS+ LF+G+FNE GL V
Sbjct: 301 VVILPDSGERYLSSVLFEGVFNEAGLPV 328


Lambda     K      H
   0.316    0.134    0.378 

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: 475
Number of extensions: 17
Number of successful extensions: 1
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: 329
Length of database: 328
Length adjustment: 28
Effective length of query: 301
Effective length of database: 300
Effective search space:    90300
Effective search space used:    90300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Dsui_2521 Dsui_2521 (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.6923.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     9e-139  447.8   0.1     1e-138  447.6   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_2521  Dsui_2521 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2521  Dsui_2521 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.6   0.1    1e-138    1e-138       2     298 .]      12     317 ..      11     317 .. 0.99

  Alignments for each domain:
  == domain 1  score: 447.6 bits;  conditional E-value: 1e-138
                         TIGR01139   2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaa 77 
                                       s+ iG+tPlvrLn ++++a a vl+k+e +nP++svk+ri++am++dae +gll +gk++ve+tsGntGiala+vaa
  lcl|FitnessBrowser__PS:Dsui_2521  12 SRSIGRTPLVRLNrVTDGAPATVLAKIEGRNPAYSVKCRIGAAMVWDAEIRGLLGPGKELVEPTSGNTGIALAFVAA 88 
                                       679**********9999************************************************************ PP

                         TIGR01139  78 argykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttap 154
                                         g  l+ltmpetmslerrkll ayGa+lvLt+g++gm gai+kaee+++++p ky+ll+qf+npanp+ih++tt+p
  lcl|FitnessBrowser__PS:Dsui_2521  89 VYGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGTKGMGGAIAKAEEIAASDPGKYVLLQQFKNPANPAIHESTTGP 165
                                       ***************************************************************************** PP

                         TIGR01139 155 eilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigagfiPk 224
                                       ei+ d+d+k+d+fv+gvGtGGtitGv++++k++++ ++ +vaveP++spvl+++      kpgphkiqGigagf+P+
  lcl|FitnessBrowser__PS:Dsui_2521 166 EIWIDTDDKVDIFVSGVGTGGTITGVSRYFKKTRGaKLWSVAVEPSASPVLTQTrngepvKPGPHKIQGIGAGFVPQ 242
                                       *********************************998*****************99999******************* PP

                         TIGR01139 225 vLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298
                                       vLd ++id + +vs+eea+++arrla+eeGi++GissGaava a ++a++ e ++k+ivvilpd+gerYls  Lf
  lcl|FitnessBrowser__PS:Dsui_2521 243 VLDLSLIDAIEQVSNEEAVAYARRLAREEGIISGISSGAAVAVASRLAQRREnAGKTIVVILPDSGERYLSSVLF 317
                                       *************************************************9999*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (328 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: 8.53
//
[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