Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 352607 BT3080 cysteine synthase A (NCBI ptt file)
Query= BRENDA::P9WP55 (310 letters) >FitnessBrowser__Btheta:352607 Length = 315 Score = 377 bits (968), Expect = e-109 Identities = 191/306 (62%), Positives = 234/306 (76%), Gaps = 2/306 (0%) Query: 3 IAEDITQLIGRTPLVRLRRV--TDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGL 60 IA +T L+G TPL+ L ++G A ++ K+E FNPA SVKDR+ +AM++ AE G+ Sbjct: 4 IARKLTDLVGNTPLLELSNYNKSNGLKARLIVKIESFNPAGSVKDRVALAMIEDAEMKGV 63 Query: 61 IKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGAD 120 + P I+EPTSGNTG+ LA V AA+GY+ +LTMP+TMS+ERR LL+A GAEL+LTPGAD Sbjct: 64 LTPGATIIEPTSGNTGVGLAFVAAAKGYKLILTMPDTMSVERRNLLKALGAELVLTPGAD 123 Query: 121 GMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTG 180 GM GAIAKAEEL + QQFENPANPA+H TT E+WRDT+GKVDI VAGVGTG Sbjct: 124 GMKGAIAKAEELKAATPGSVILQQFENPANPAMHLRTTGLEIWRDTEGKVDIFVAGVGTG 183 Query: 181 GTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEI 240 GTI+GV + +K R PS + VAVEPA SPVLSGG+ GPH IQGIGAGFVP + +VDEI Sbjct: 184 GTISGVGEALKMRDPSVKAVAVEPADSPVLSGGKPGPHKIQGIGAGFVPKTYNASVVDEI 243 Query: 241 ITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYL 300 I V N+DA+ +R LA EEGLLVGISSGAA AA ++A+RPEN GK+IV +LPD GERYL Sbjct: 244 IQVQNDDAIRTSRALAEEEGLLVGISSGAAVYAATELAKRPENEGKMIVALLPDTGERYL 303 Query: 301 STPLFA 306 ST L+A Sbjct: 304 STILYA 309 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: 348 Number of extensions: 11 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: 315 Length adjustment: 27 Effective length of query: 283 Effective length of database: 288 Effective search space: 81504 Effective search space used: 81504 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 352607 BT3080 (cysteine synthase A (NCBI ptt file))
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.24082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-144 466.0 0.8 2.9e-144 465.8 0.8 1.0 1 lcl|FitnessBrowser__Btheta:352607 BT3080 cysteine synthase A (NCBI Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:352607 BT3080 cysteine synthase A (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.8 0.8 2.9e-144 2.9e-144 2 298 .] 9 308 .. 8 308 .. 0.98 Alignments for each domain: == domain 1 score: 465.8 bits; conditional E-value: 2.9e-144 TIGR01139 2 seliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 ++l+GntPl++L ++ ka+++vk+es+nP++svkdr+alamiedae +g+l++g ti+e+tsGntG++la+ lcl|FitnessBrowser__Btheta:352607 9 TDLVGNTPLLELSnynKSNGLKARLIVKIESFNPAGSVKDRVALAMIEDAEMKGVLTPGATIIEPTSGNTGVGLAF 84 689*********8655677899****************************************************** PP TIGR01139 75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrk 150 vaaa+gykliltmp+tms+err+llka+GaelvLt+ga gmkgai+kaeel ++tp + +l+qfenpanp++h + lcl|FitnessBrowser__Btheta:352607 85 VAAAKGYKLILTMPDTMSVERRNLLKALGAELVLTPGADGMKGAIAKAEELKAATPGSV-ILQQFENPANPAMHLR 159 ********************************************************666.**************** PP TIGR01139 151 ttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigagfiPkvL 226 tt+ ei++d++gk+d+fvagvGtGGti+Gvge+lk +p++k+vavePa+spvlsggkpgphkiqGigagf+Pk lcl|FitnessBrowser__Btheta:352607 160 TTGLEIWRDTEGKVDIFVAGVGTGGTISGVGEALKMRDPSVKAVAVEPADSPVLSGGKPGPHKIQGIGAGFVPKTY 235 **************************************************************************** PP TIGR01139 227 dkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 + +v+de+i+v++++ai+t+r la+eeG+lvGissGaav+aa+++ak++e ++k+iv++lpdtgerYlst L+ lcl|FitnessBrowser__Btheta:352607 236 NASVVDEIIQVQNDDAIRTSRALAEEEGLLVGISSGAAVYAATELAKRPEnEGKMIVALLPDTGERYLSTILY 308 **************************************************99******************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (315 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.73 // [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