Alignments for a candidate for cysK in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Desulfovibrio vulgaris Miyazaki F

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 8501944 DvMF_2658 cysteine synthase (RefSeq)

Query= BRENDA::P9WP55
         (310 letters)



>FitnessBrowser__Miya:8501944
          Length = 310

 Score =  368 bits (944), Expect = e-106
 Identities = 187/310 (60%), Positives = 226/310 (72%)

Query: 1   MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGL 60
           M IA D+T+L+GRTPLVRL RV++G  A++VAKLEF NP  SVKDRI +AM+  A + G 
Sbjct: 1   MEIARDMTELVGRTPLVRLNRVSEGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERGE 60

Query: 61  IKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGAD 120
           + P  +++EPTSGNTG+ LA V A RG   VLTMPE+MS ER+ LLR +GA L+LTP + 
Sbjct: 61  LAPGGLLVEPTSGNTGVGLAFVAAVRGLTLVLTMPESMSNERKALLRGFGARLVLTPASK 120

Query: 121 GMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTG 180
           GM GAI +AE +        +  QF NP NP +HR TTAEE+W DTDGKVD  VAGVGTG
Sbjct: 121 GMRGAIEEAERIVAETPGAVMLGQFVNPDNPLVHRKTTAEEIWADTDGKVDAFVAGVGTG 180

Query: 181 GTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEI 240
           GT+TG  + ++E  P  +  AVEP  SPVLSGG  GPHPIQGIGAGFVPPVLD  + DEI
Sbjct: 181 GTVTGTGRRLRELNPDIKVFAVEPDESPVLSGGAPGPHPIQGIGAGFVPPVLDTKVYDEI 240

Query: 241 ITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYL 300
           I V  +DAL  ARRL REEG+L G+SSGA   AA+ VARRPE AGK +V V+ D GERYL
Sbjct: 241 IRVPGKDALVTARRLLREEGILCGVSSGANAFAAMAVARRPEMAGKRVVFVVCDTGERYL 300

Query: 301 STPLFADVAD 310
           STPLF ++ D
Sbjct: 301 STPLFTEMPD 310


Lambda     K      H
   0.318    0.136    0.383 

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: 343
Number of extensions: 19
Number of successful extensions: 2
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: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 8501944 DvMF_2658 (cysteine synthase (RefSeq))
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.22096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.3e-136  438.0   0.0   9.3e-136  437.9   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501944  DvMF_2658 cysteine synthase (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501944  DvMF_2658 cysteine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.9   0.0  9.3e-136  9.3e-136       2     298 .]       8     305 ..       7     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.9 bits;  conditional E-value: 9.3e-136
                         TIGR01139   2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaa 77 
                                       +el+G+tPlvrLn + e+++aev++kle++nP++svkdrialami  a ++g l +g  +ve+tsGntG++la+vaa
  lcl|FitnessBrowser__Miya:8501944   8 TELVGRTPLVRLNrVSEGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERGELAPGGLLVEPTSGNTGVGLAFVAA 84 
                                       799**********999************************************************************* PP

                         TIGR01139  78 argykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttap 154
                                        rg++l+ltmpe+ms er++ll+ +Ga+lvLt++++gm+gaie+ae +v+etp   ++l qf np np +hrktta+
  lcl|FitnessBrowser__Miya:8501944  85 VRGLTLVLTMPESMSNERKALLRGFGARLVLTPASKGMRGAIEEAERIVAETP-GAVMLGQFVNPDNPLVHRKTTAE 160
                                       *****************************************************.556******************** PP

                         TIGR01139 155 eilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigagfiPkvLdkevi 231
                                       ei+ d+dgk+dafvagvGtGGt+tG+g+ l+e +pdikv+aveP espvlsgg pgph iqGigagf+P vLd++v+
  lcl|FitnessBrowser__Miya:8501944 161 EIWADTDGKVDAFVAGVGTGGTVTGTGRRLRELNPDIKVFAVEPDESPVLSGGAPGPHPIQGIGAGFVPPVLDTKVY 237
                                       ***************************************************************************** PP

                         TIGR01139 232 devikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298
                                       de+i+v   +a+ tarrl +eeGil G+ssGa+ +aa+ va+++e ++k++v +++dtgerYlst+Lf
  lcl|FitnessBrowser__Miya:8501944 238 DEIIRVPGKDALVTARRLLREEGILCGVSSGANAFAAMAVARRPEmAGKRVVFVVCDTGERYLSTPLF 305
                                       *********************************************9*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (310 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: 00:00:00.00
# Mc/sec: 11.28
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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