Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 206086 DVU0663 cysteine synthase A
Query= BRENDA::P9WP55 (310 letters) >MicrobesOnline__882:206086 Length = 308 Score = 363 bits (933), Expect = e-105 Identities = 183/306 (59%), Positives = 222/306 (72%) Query: 1 MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGL 60 M IA +T L+G+TP+VRL +VT G VA++VAKLE FNP +SVKDRI + M++AA G Sbjct: 1 MDIASSMTDLVGKTPMVRLNKVTLGCVAEVVAKLENFNPCSSVKDRIALNMVEAAIARGE 60 Query: 61 IKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGAD 120 I P +++EPTSGNTG+ LA VCA RG + VLTMPE+MS ERR LL+A+G L+LTP A Sbjct: 61 IAPGAVLVEPTSGNTGVGLAFVCAVRGLKLVLTMPESMSAERRALLKAFGTTLVLTPAAK 120 Query: 121 GMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTG 180 GM GA+ +AE + + QQF NP NPA H TT E+W DTDG +D VAGVGTG Sbjct: 121 GMRGAVEEAERIVADTPGAVMLQQFANPDNPAAHEATTGPEIWADTDGMIDCFVAGVGTG 180 Query: 181 GTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEI 240 GTITG + +K R P R +AVEPA S VLSGG GPH IQGIGAGFVPPVLD + DE+ Sbjct: 181 GTITGTGRYLKGRNPDIRVIAVEPAESAVLSGGAPGPHAIQGIGAGFVPPVLDTSVYDEV 240 Query: 241 ITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYL 300 + V DAL +ARRL +EEG+L GISSGA AA+ ARRPENAGK +V ++ D GERYL Sbjct: 241 MPVPGADALTMARRLLQEEGILCGISSGANVHAAIAYARRPENAGKRVVCIICDTGERYL 300 Query: 301 STPLFA 306 STPLFA Sbjct: 301 STPLFA 306 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: 336 Number of extensions: 13 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: 310 Length of database: 308 Length adjustment: 27 Effective length of query: 283 Effective length of database: 281 Effective search space: 79523 Effective search space used: 79523 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 206086 DVU0663 (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.6799.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-138 447.3 0.0 1.4e-138 447.2 0.0 1.0 1 lcl|MicrobesOnline__882:206086 DVU0663 cysteine synthase A Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206086 DVU0663 cysteine synthase A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.2 0.0 1.4e-138 1.4e-138 2 298 .] 8 305 .. 7 305 .. 0.99 Alignments for each domain: == domain 1 score: 447.2 bits; conditional E-value: 1.4e-138 TIGR01139 2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaar 79 ++l+G+tP+vrLn ++ ++ aev++kle +nP+ssvkdrial+m+e a +g + +g ++ve+tsGntG++la+v+a r lcl|MicrobesOnline__882:206086 8 TDLVGKTPMVRLNkVTLGCVAEVVAKLENFNPCSSVKDRIALNMVEAAIARGEIAPGAVLVEPTSGNTGVGLAFVCAVR 86 789**********999*************************************************************** PP TIGR01139 80 gykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttapeilk 158 g+kl+ltmpe+ms err+llka+G+ lvLt++a+gm+ga+e+ae +v++tp ++l+qf+np np++h++tt+pei+ lcl|MicrobesOnline__882:206086 87 GLKLVLTMPESMSAERRALLKAFGTTLVLTPAAKGMRGAVEEAERIVADTP-GAVMLQQFANPDNPAAHEATTGPEIWA 164 ***************************************************.556************************ PP TIGR01139 159 dldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigagfiPkvLdkevidevikv 237 d+dg +d fvagvGtGGtitG+g++lk +pdi+v+avePaes+vlsgg pgph+iqGigagf+P vLd++v+dev+ v lcl|MicrobesOnline__882:206086 165 DTDGMIDCFVAGVGTGGTITGTGRYLKGRNPDIRVIAVEPAESAVLSGGAPGPHAIQGIGAGFVPPVLDTSVYDEVMPV 243 ******************************************************************************* PP TIGR01139 238 sdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 +a+++arrl +eeGil GissGa+v aa+ a+++e ++k++v+i++dtgerYlst+Lf lcl|MicrobesOnline__882:206086 244 PGADALTMARRLLQEEGILCGISSGANVHAAIAYARRPEnAGKRVVCIICDTGERYLSTPLF 305 **************************************99*********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (308 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: 9.43 // [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