Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)
Query= BRENDA::P0ABK5 (323 letters) >FitnessBrowser__Keio:16513 Length = 323 Score = 626 bits (1614), Expect = 0.0 Identities = 323/323 (100%), Positives = 323/323 (100%) Query: 1 MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60 MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK Sbjct: 1 MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60 Query: 61 PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120 PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM Sbjct: 61 PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120 Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG Sbjct: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180 Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD Sbjct: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240 Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP Sbjct: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300 Query: 301 SSGERYLSTALFADLFTEKELQQ 323 SSGERYLSTALFADLFTEKELQQ Sbjct: 301 SSGERYLSTALFADLFTEKELQQ 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: 507 Number of extensions: 12 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: 323 Length of database: 323 Length adjustment: 28 Effective length of query: 295 Effective length of database: 295 Effective search space: 87025 Effective search space used: 87025 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 16513 b2414 (cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI))
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.17706.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-150 485.8 1.1 2.6e-150 485.7 1.1 1.0 1 lcl|FitnessBrowser__Keio:16513 b2414 cysteine synthase A, O-ace Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.7 1.1 2.6e-150 2.6e-150 2 298 .] 9 312 .. 8 312 .. 0.98 Alignments for each domain: == domain 1 score: 485.7 bits; conditional E-value: 2.6e-150 TIGR01139 2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaarg 80 s +iG+tPlvrLn +++ ++++l+k+es+nPs+svk+ri+++mi+daek+g+lk+g ++ve+tsGntGiala+vaaarg lcl|FitnessBrowser__Keio:16513 9 SLTIGHTPLVRLN-RIG-NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLKPGVELVEPTSGNTGIALAYVAAARG 85 569**********.666.89*********************************************************** PP TIGR01139 81 ykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttapeilkd 159 ykl+ltmpetms+errkllka+Ga+lvLt+ga+gmkgai+kaee+v+++p+kylll+qf+npanpeih+ktt+pei++d lcl|FitnessBrowser__Keio:16513 86 YKLTLTMPETMSIERRKLLKALGANLVLTEGAKGMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWED 164 ******************************************************************************* PP TIGR01139 160 ldgkldafvagvGtGGtitGvgevlkekkp..dikvvavePaespvlsgg......kpgphkiqGigagfiPkvLdkev 230 +dg++d+f+agvGtGGt+tGv++++k +k+ d+ +vaveP++spv++++ kpgphkiqGigagfiP++Ld ++ lcl|FitnessBrowser__Keio:16513 165 TDGQVDVFIAGVGTGGTLTGVSRYIKGTKGktDLISVAVEPTDSPVIAQAlageeiKPGPHKIQGIGAGFIPANLDLKL 243 **************************99887799***************9999************************** PP TIGR01139 231 idevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 +d+vi +++eeai+tarrl++eeGil+GissGaavaaalk++++++ ++k+ivvilp++gerYlstaLf lcl|FitnessBrowser__Keio:16513 244 VDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESfTNKNIVVILPSSGERYLSTALF 312 ********************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (323 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: 8.18 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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