Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 7024369 Shewana3_1561 cysteine synthase (RefSeq)
Query= BRENDA::P0ABK5 (323 letters) >FitnessBrowser__ANA3:7024369 Length = 322 Score = 483 bits (1242), Expect = e-141 Identities = 244/320 (76%), Positives = 275/320 (85%), Gaps = 1/320 (0%) Query: 1 MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60 MSKIFEDNS TIG+TPLVRLNR+ G++LAKVE+RNPSFSVKCRIGANMIWDAEK+G+L Sbjct: 1 MSKIFEDNSYTIGNTPLVRLNRVSQGKVLAKVEARNPSFSVKCRIGANMIWDAEKKGLLT 60 Query: 61 PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120 EL+EPTSGNTGIALAYVAAARGYKLTLTMP TMS+ERRKLLKALGANLVLTEGAKGM Sbjct: 61 KDHELIEPTSGNTGIALAYVAAARGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGM 120 Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180 KGAI KAEEI S PEKY++LQQF+NPANPEIHEKTTGPEIW DTDG VDVF+AGVGTGG Sbjct: 121 KGAIDKAEEIRQSAPEKYIMLQQFNNPANPEIHEKTTGPEIWNDTDGAVDVFVAGVGTGG 180 Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240 T+TGVSRY+K GK + SVAVEP DSPVI Q LAG ++PGPHKIQGIGAGFIP NLD Sbjct: 181 TITGVSRYLKKVAGKA-ITSVAVEPADSPVITQTLAGLPVQPGPHKIQGIGAGFIPGNLD 239 Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300 L+L+D+V +TN+EAI ARRLM+EEGIL GISSGAAV AA ++ F +KNIVVILP Sbjct: 240 LELIDRVETVTNDEAIDMARRLMQEEGILVGISSGAAVVAANRIAALPEFADKNIVVILP 299 Query: 301 SSGERYLSTALFADLFTEKE 320 S+ ERYLS+ LF F ++E Sbjct: 300 SAAERYLSSVLFQGQFGDEE 319 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: 414 Number of extensions: 13 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: 323 Length of database: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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 7024369 Shewana3_1561 (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.949.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-148 477.6 0.8 8.4e-148 477.4 0.8 1.0 1 lcl|FitnessBrowser__ANA3:7024369 Shewana3_1561 cysteine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024369 Shewana3_1561 cysteine synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.4 0.8 8.4e-148 8.4e-148 2 298 .] 9 311 .. 8 311 .. 0.98 Alignments for each domain: == domain 1 score: 477.4 bits; conditional E-value: 8.4e-148 TIGR01139 2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaa 78 s +iGntPlvrLn +++vl+k+e +nPs+svk+ri+++mi+daek+gll+k+++++e+tsGntGiala+vaaa lcl|FitnessBrowser__ANA3:7024369 9 SYTIGNTPLVRLN--RVSQGKVLAKVEARNPSFSVKCRIGANMIWDAEKKGLLTKDHELIEPTSGNTGIALAYVAAA 83 679**********..44479********************************************************* PP TIGR01139 79 rgykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttape 155 rgykl+ltmp+tmslerrkllka+Ga+lvLt+ga+gmkgai+kaee+ ++ p+ky++l+qf+npanpeih+ktt+pe lcl|FitnessBrowser__ANA3:7024369 84 RGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGMKGAIDKAEEIRQSAPEKYIMLQQFNNPANPEIHEKTTGPE 160 ***************************************************************************** PP TIGR01139 156 ilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigagfiPkv 225 i++d+dg++d+fvagvGtGGtitGv+++lk+ + i++vavePa+spv++++ +pgphkiqGigagfiP + lcl|FitnessBrowser__ANA3:7024369 161 IWNDTDGAVDVFVAGVGTGGTITGVSRYLKKVAGkAITSVAVEPADSPVITQTlaglpvQPGPHKIQGIGAGFIPGN 237 *******************************99879****************99*********************** PP TIGR01139 226 LdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 Ld e+id+v +v+++eai++arrl++eeGilvGissGaav+aa ++a +e +dk+ivvilp+++erYls Lf lcl|FitnessBrowser__ANA3:7024369 238 LDLELIDRVETVTNDEAIDMARRLMQEEGILVGISSGAAVVAANRIAALPEfADKNIVVILPSAAERYLSSVLF 311 ***********************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (322 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: 00:00:00.00 # Mc/sec: 11.29 // [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