Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF3511 HP15_3453 cysteine synthase A
Query= BRENDA::P0A1E3 (323 letters) >FitnessBrowser__Marino:GFF3511 Length = 323 Score = 463 bits (1191), Expect = e-135 Identities = 229/321 (71%), Positives = 272/321 (84%), Gaps = 2/321 (0%) Query: 1 MSKIYEDNSLTIGHTPLVRLNRIGNGR-ILAKVESRNPSFSVKCRIGANMIWDAEKRGVL 59 M++IYEDNSL+IG+TPLVRLNR+ +G I AK+E RNP++SVKCRIG+ MIWDAEKRG L Sbjct: 1 MARIYEDNSLSIGNTPLVRLNRVNDGATIWAKIEGRNPAYSVKCRIGSAMIWDAEKRGTL 60 Query: 60 KPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKG 119 K G+ +VEPTSGNTGIALAYVAAARGYKL LTMP +MS+ERRK+LKALGA LVLTE AKG Sbjct: 61 KAGMTIVEPTSGNTGIALAYVAAARGYKLILTMPASMSLERRKVLKALGAELVLTEPAKG 120 Query: 120 MKGAIQKAEEIVASDPQKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFISGVGTG 179 M GAI KAEEI +SDP Y L QQF NPANP IHE TTGPEIWEDTDG++D+F++GVGTG Sbjct: 121 MPGAIAKAEEIFSSDPDNYFLPQQFQNPANPRIHEDTTGPEIWEDTDGEIDIFVAGVGTG 180 Query: 180 GTLTGVTRYIKGTKGKTDLITVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPGNL 239 GTLTGV+RYIKGTKGK + T+AVEPTDSPVI Q + GE+IKP PHKIQGIGAGF+P NL Sbjct: 181 GTLTGVSRYIKGTKGK-QIATIAVEPTDSPVITQMMNGEDIKPAPHKIQGIGAGFVPKNL 239 Query: 240 DLKLIDKVVGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVIL 299 DL+++D+V ++NEEA+ A RLM+EEGIL GIS GAAVAAA+++ + + KNIVV+L Sbjct: 240 DLEMVDQVETVSNEEAMDMAHRLMQEEGILCGISCGAAVAAAVRISKQPEYQGKNIVVVL 299 Query: 300 PSSGERYLSTALFADLFTEKE 320 P + ERYLSTALFA F E+E Sbjct: 300 PDTAERYLSTALFAGQFGEQE 320 Lambda K H 0.313 0.133 0.370 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: 17 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: 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 GFF3511 HP15_3453 (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.2388.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-145 467.5 0.2 9.9e-145 467.3 0.2 1.0 1 lcl|FitnessBrowser__Marino:GFF3511 HP15_3453 cysteine synthase A Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3511 HP15_3453 cysteine synthase A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.3 0.2 9.9e-145 9.9e-145 3 298 .] 10 312 .. 8 312 .. 0.98 Alignments for each domain: == domain 1 score: 467.3 bits; conditional E-value: 9.9e-145 TIGR01139 3 eliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaa 77 iGntPlvrLn + + a + +k+e +nP++svk+ri+ ami+daek+g+lk g tive+tsGntGiala+vaa lcl|FitnessBrowser__Marino:GFF3511 10 LSIGNTPLVRLN-RVNDGATIWAKIEGRNPAYSVKCRIGSAMIWDAEKRGTLKAGMTIVEPTSGNTGIALAYVAA 83 68**********.66679********************************************************* PP TIGR01139 78 argykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrktt 152 argykliltmp++mslerrk+lka+GaelvLt++a+gm gai+kaee+ +++p++y+l++qf+npanp+ih+ tt lcl|FitnessBrowser__Marino:GFF3511 84 ARGYKLILTMPASMSLERRKVLKALGAELVLTEPAKGMPGAIAKAEEIFSSDPDNYFLPQQFQNPANPRIHEDTT 158 *************************************************************************** PP TIGR01139 153 apeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigag 220 +pei++d+dg++d+fvagvGtGGt+tGv++++k +k+ +i +aveP++spv+++ kp phkiqGigag lcl|FitnessBrowser__Marino:GFF3511 159 GPEIWEDTDGEIDIFVAGVGTGGTLTGVSRYIKGTKGkQIATIAVEPTDSPVITQMmngediKPAPHKIQGIGAG 233 **********************************99989****************9999999************* PP TIGR01139 221 fiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYls 294 f+Pk+Ld e++d+v +vs+eea+++a+rl++eeGil Gis Gaavaaa++++k++e ++k+ivv+lpdt+erYls lcl|FitnessBrowser__Marino:GFF3511 234 FVPKNLDLEMVDQVETVSNEEAMDMAHRLMQEEGILCGISCGAAVAAAVRISKQPEyQGKNIVVVLPDTAERYLS 308 *************************************************************************** PP TIGR01139 295 taLf 298 taLf lcl|FitnessBrowser__Marino:GFF3511 309 TALF 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: 00:00:00.00 # Mc/sec: 11.46 // [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