Align O-ureido-L-serine synthase; Cysteine synthase homolog DscD; O-acetylserine sulfhydrylase; EC 2.6.99.3; EC 2.5.1.47 (characterized)
to candidate WP_106717134.1 CU100_RS14020 cysteine synthase A
Query= SwissProt::D2Z027 (324 letters) >NCBI__GCF_003010935.1:WP_106717134.1 Length = 362 Score = 317 bits (812), Expect = 3e-91 Identities = 169/330 (51%), Positives = 216/330 (65%), Gaps = 20/330 (6%) Query: 3 LFNSILDTIGRTPIVRLQRMAPEHTSVYVKVESFNPGGSVKDRLALSVVLDAEAKGLLKP 62 LF+SILDTIG TP VR+ +AP+H ++YVK E FNP SVKDRLAL+++ +AE G LKP Sbjct: 16 LFDSILDTIGDTPAVRINNLAPDHVTIYVKAEFFNPASSVKDRLALNIIEEAERNGTLKP 75 Query: 63 GDTIVECTSGNVGIALAMVAAARGYRFVAVMGDTYSVERRKLIRAYGGKLVLFPGHLGSK 122 G T+VE TSGN GI LAMV A +GY V M D++S+ERRKL+R G K+VL P Sbjct: 76 GQTVVEATSGNTGIGLAMVCAQKGYPLVVTMADSFSIERRKLMRMLGAKVVLTPRAQKGF 135 Query: 123 GGNLIADELAEKYGWFRARQFDNPANPSYHRETTASEILADFAGKRLDHFVTGFGTTGTL 182 G A ELAE GWF ARQF+ AN H TTA EI+ DFAG RLD+FVTG+GT GT+ Sbjct: 136 GMYQKAVELAEMNGWFLARQFETEANADIHEATTAREIINDFAGSRLDYFVTGYGTGGTV 195 Query: 183 TGVGQMLRVARPEVRVVALEPSNAAMLARGE----------------WSPHQIQGLAPNF 226 +GVG++LR RPE R+V EP+NA +L G+ + PH IQG P+F Sbjct: 196 SGVGRVLRRERPETRIVLSEPANAQLLGSGKVQVRGAGGAPAASHPAFEPHPIQGWTPDF 255 Query: 227 VPGVL----DRSVIDDLVTMDEVTARDTSRRLAAEEGIFAGISAGATVATALSIAEHAPE 282 +P VL D + D ++ + +R LA +EG+F GIS GAT A A SIAE A Sbjct: 256 IPNVLQEAIDHKLYDQVMPIAGPEGIKWARALAQKEGMFTGISGGATFAVAHSIAETAAA 315 Query: 283 GTVLLAMLPDTGERYLSTFLFDGVDEGSDD 312 G+V+L MLPDTGERY++T LF+G++ D+ Sbjct: 316 GSVILCMLPDTGERYMTTPLFEGIETEMDE 345 Lambda K H 0.319 0.136 0.395 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: 317 Number of extensions: 13 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: 324 Length of database: 362 Length adjustment: 29 Effective length of query: 295 Effective length of database: 333 Effective search space: 98235 Effective search space used: 98235 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_106717134.1 CU100_RS14020 (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.3980528.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-110 353.3 0.0 6.5e-110 353.0 0.0 1.1 1 NCBI__GCF_003010935.1:WP_106717134.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106717134.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.0 0.0 6.5e-110 6.5e-110 2 298 .] 21 336 .. 20 336 .. 0.97 Alignments for each domain: == domain 1 score: 353.0 bits; conditional E-value: 6.5e-110 TIGR01139 2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 ++iG+tP vr+n ++ ++ ++vk e++nP+ssvkdr+al++ie+ae++g+lk+g+t+veatsGntGi+lam NCBI__GCF_003010935.1:WP_106717134.1 21 LDTIGDTPAVRINNLAPDHVTIYVKAEFFNPASSVKDRLALNIIEEAERNGTLKPGQTVVEATSGNTGIGLAM 93 579**********99999******************************************************* PP TIGR01139 75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpei 147 v+a++gy l++tm++++s+errkl++++Ga++vLt+ a++ g+ +ka el+e ++ ++l++qfe +an +i NCBI__GCF_003010935.1:WP_106717134.1 94 VCAQKGYPLVVTMADSFSIERRKLMRMLGAKVVLTPRAQKGFGMYQKAVELAEMNG--WFLARQFETEANADI 164 *******************************************************9..99************* PP TIGR01139 148 hrkttapeilkdldgk.ldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsgg............ 207 h++tta+ei++d+ g+ ld fv+g+GtGGt++Gvg+vl++++p+ ++v +ePa++++l g NCBI__GCF_003010935.1:WP_106717134.1 165 HEATTAREIINDFAGSrLDYFVTGYGTGGTVSGVGRVLRRERPETRIVLSEPANAQLLGSGkvqvrgaggapa 237 *************9988*****************************************8888*********** PP TIGR01139 208 ....kpgphkiqGigagfiPkvL....dkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkva 272 ph iqG++++fiP+vL d++++d+v+ + e i+ ar la++eG+++Gis+Ga+ a a +a NCBI__GCF_003010935.1:WP_106717134.1 238 ashpAFEPHPIQGWTPDFIPNVLqeaiDHKLYDQVMPIAGPEGIKWARALAQKEGMFTGISGGATFAVAHSIA 310 *988889**************9844446789****************************************** PP TIGR01139 273 kklekdkkivvilpdtgerYlstaLf 298 + ++++ +i+++lpdtgerY++t+Lf NCBI__GCF_003010935.1:WP_106717134.1 311 ETAAAGSVILCMLPDTGERYMTTPLF 336 *************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (362 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: 16.01 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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