Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 6937338 Sama_1508 cysteine synthase A (RefSeq)
Query= BRENDA::P0ABK5 (323 letters) >FitnessBrowser__SB2B:6937338 Length = 322 Score = 487 bits (1254), Expect = e-142 Identities = 246/320 (76%), Positives = 278/320 (86%), Gaps = 1/320 (0%) Query: 1 MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60 MSKIFEDNS TIG+TPLVRLNR+ NG++LAKVE+RNPSFSVKCRIGANMIWDAEKRGVL Sbjct: 1 MSKIFEDNSYTIGNTPLVRLNRVSNGKVLAKVEARNPSFSVKCRIGANMIWDAEKRGVLT 60 Query: 61 PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120 EL+EPTSGNTGIALAYVAAARGYKLTLTMP TMS+ERRKLLKALGANLVLTEGAKGM Sbjct: 61 KDKELIEPTSGNTGIALAYVAAARGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGM 120 Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180 KGAI+KAEEI S PEKY+LLQQF NPANPEIHEKTTGPEIW DTDG VDV +AGVGTGG Sbjct: 121 KGAIEKAEEIRQSAPEKYVLLQQFDNPANPEIHEKTTGPEIWNDTDGAVDVVVAGVGTGG 180 Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240 T+TGVSRYIK +GK ++SVAVEP DSPVI+Q LAG+ ++PGPHKIQGIGAGFIP NLD Sbjct: 181 TITGVSRYIKKAQGKA-IVSVAVEPVDSPVISQTLAGQPVQPGPHKIQGIGAGFIPGNLD 239 Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300 L+L+D+V ++NE+AI A RLM+EEGIL GISSGAAV AA ++ F +KNIVVILP Sbjct: 240 LELIDRVETVSNEDAIEMAHRLMKEEGILVGISSGAAVVAANRIAALPEFADKNIVVILP 299 Query: 301 SSGERYLSTALFADLFTEKE 320 S+ ERYLS+ LF F ++E Sbjct: 300 SAAERYLSSVLFQGQFGDQE 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: 409 Number of extensions: 16 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 6937338 Sama_1508 (cysteine synthase A (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.18110.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-147 475.1 1.2 4.8e-147 474.9 1.2 1.0 1 lcl|FitnessBrowser__SB2B:6937338 Sama_1508 cysteine synthase A (R Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937338 Sama_1508 cysteine synthase A (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.9 1.2 4.8e-147 4.8e-147 2 298 .] 9 311 .. 8 311 .. 0.98 Alignments for each domain: == domain 1 score: 474.9 bits; conditional E-value: 4.8e-147 TIGR01139 2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaa 78 s +iGntPlvrLn +++vl+k+e +nPs+svk+ri+++mi+daek+g+l+k+k+++e+tsGntGiala+vaaa lcl|FitnessBrowser__SB2B:6937338 9 SYTIGNTPLVRLN--RVSNGKVLAKVEARNPSFSVKCRIGANMIWDAEKRGVLTKDKELIEPTSGNTGIALAYVAAA 83 679**********..44579********************************************************* PP TIGR01139 79 rgykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttape 155 rgykl+ltmp+tmslerrkllka+Ga+lvLt+ga+gmkgaiekaee+ ++ p+ky+ll+qf+npanpeih+ktt+pe lcl|FitnessBrowser__SB2B:6937338 84 RGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGMKGAIEKAEEIRQSAPEKYVLLQQFDNPANPEIHEKTTGPE 160 ***************************************************************************** PP TIGR01139 156 ilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigagfiPkv 225 i++d+dg++d++vagvGtGGtitGv++++k++++ i +vaveP++spv+s++ +pgphkiqGigagfiP + lcl|FitnessBrowser__SB2B:6937338 161 IWNDTDGAVDVVVAGVGTGGTITGVSRYIKKAQGkAIVSVAVEPVDSPVISQTlagqpvQPGPHKIQGIGAGFIPGN 237 *******************************99978999*************99*********************** PP TIGR01139 226 LdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 Ld e+id+v +vs+e+aie+a+rl+keeGilvGissGaav+aa ++a +e +dk+ivvilp+++erYls Lf lcl|FitnessBrowser__SB2B:6937338 238 LDLELIDRVETVSNEDAIEMAHRLMKEEGILVGISSGAAVVAANRIAALPEfADKNIVVILPSAAERYLSSVLF 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.29 // [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