Align D-serine dehydratase; D-serine deaminase; DSD; EC 4.3.1.18 (characterized)
to candidate WP_193345603.1 DHAF_RS14450 D-serine ammonia-lyase
Query= SwissProt::Q8FFF4 (442 letters) >NCBI__GCF_000021925.1:WP_193345603.1 Length = 444 Score = 507 bits (1306), Expect = e-148 Identities = 264/442 (59%), Positives = 311/442 (70%), Gaps = 5/442 (1%) Query: 5 KMNSLIAQYPLVEDLVALKETTWFNPGTTSLAEGLP-YVGLTEQDVQDAHARLSRFAPYL 63 K +I P+V+DL A +E W NP + E G++ D+ DA RL RFAPYL Sbjct: 4 KSPEVIPHTPVVQDLRAAREIFWINPHYRATKEFKEAQFGISLSDIHDAEERLRRFAPYL 63 Query: 64 AKAFPETAAAGGIIESELVAIPAMQKRLEKEYQQPIAGQLLLKKDSHLPISGSIKARGGI 123 AKAFPET A G+IES +V I MQ LE Y I G + LK D LPISGSIKARGGI Sbjct: 64 AKAFPETQPAQGLIESPIVPIKRMQSYLESRYGVQIPGDIWLKCDHQLPISGSIKARGGI 123 Query: 124 YEVLAHAEKLALEAGLLTLEDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSARIG 183 YEVL HAE+ ++ GLLT EDDY++L F+ S Y IAVGSTGNLGLSIG+M A +G Sbjct: 124 YEVLKHAEETLIKQGLLTREDDYARLKDSSFRDVLSHYKIAVGSTGNLGLSIGVMGAELG 183 Query: 184 FKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRT 243 FKVTVHMSADA+ WKKA LRS GV V+EY DY AVEEGR+ A+ D C FIDDENSR Sbjct: 184 FKVTVHMSADAKGWKKALLRSKGVEVIEYTSDYSKAVEEGRRQAEGDSRCHFIDDENSRD 243 Query: 244 LFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFF 303 LFLGY+VAG RLK Q + R VDAD+PLFVYLPCGVGGGPGGV FGLK F +HVHCFF Sbjct: 244 LFLGYAVAGLRLKEQLEKLNRKVDADHPLFVYLPCGVGGGPGGVTFGLKQVFQEHVHCFF 303 Query: 304 AEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFYTL 363 AEPTHSPCM+LG+ TGLHD I+VQDIG+DN T ADGLAVGRAS FVG+ M LL G +T+ Sbjct: 304 AEPTHSPCMVLGLATGLHDGIAVQDIGLDNKTEADGLAVGRASRFVGKIMAGLLSGAFTV 363 Query: 364 SDQTMYDMLGWLAQEEGIRLEPSALAGMAGSQRVC---ASVSYQQMHGFSAEQLRNATHL 420 D ++ +L L EGI+ EPSALAGMAG R+ + Y + H E L+ THL Sbjct: 364 EDAELFRLLQALDHAEGIQCEPSALAGMAGPARLLLCKEGLQYIREHRLE-EGLKKGTHL 422 Query: 421 VWATGGGMVPEEEMNQYLAKGR 442 +WATGG +VPEE M YL++G+ Sbjct: 423 IWATGGSLVPEEVMKDYLSRGK 444 Lambda K H 0.319 0.135 0.397 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: 568 Number of extensions: 18 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: 442 Length of database: 444 Length adjustment: 32 Effective length of query: 410 Effective length of database: 412 Effective search space: 168920 Effective search space used: 168920 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: 51 (24.3 bits)
Align candidate WP_193345603.1 DHAF_RS14450 (D-serine ammonia-lyase)
to HMM TIGR02035 (dsdA: D-serine ammonia-lyase (EC 4.3.1.18))
# 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.carbon/TIGR02035.hmm # target sequence database: /tmp/gapView.727771.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02035 [M=431] Accession: TIGR02035 Description: D_Ser_am_lyase: D-serine ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-204 664.3 0.0 4.2e-204 664.1 0.0 1.0 1 NCBI__GCF_000021925.1:WP_193345603.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021925.1:WP_193345603.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 664.1 0.0 4.2e-204 4.2e-204 3 431 .] 10 440 .. 8 440 .. 0.98 Alignments for each domain: == domain 1 score: 664.1 bits; conditional E-value: 4.2e-204 TIGR02035 3 lkeplikdlidlkevewanpkkaslae.alkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiieselv 74 ++p+++dl +++e++w+np+ +++e ++++ ++ +++++ae+rl+rfapy+ak+fpet+ ++G+ies++v NCBI__GCF_000021925.1:WP_193345603.1 10 PHTPVVQDLRAAREIFWINPHYRATKEfKEAQFGISLSDIHDAEERLRRFAPYLAKAFPETQPAQGLIESPIV 82 578*****************9988777357899**************************************** PP TIGR02035 75 evaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklaeeefk 147 ++++++ le +y +++G ++lk+d++lpisGsikarGGiyevlkhae+ +++Gll+ +ddy++l++++f+ NCBI__GCF_000021925.1:WP_193345603.1 83 PIKRMQSYLESRYGVQIPGDIWLKCDHQLPISGSIKARGGIYEVLKHAEETLIKQGLLTREDDYARLKDSSFR 155 ************************************************************************* PP TIGR02035 148 dffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeae 220 d +s+ykiavGstGnlGlsiG+++a lGfkvtvhmsadak wkk++lrskGv+v+ey sdyskaveeGr++ae NCBI__GCF_000021925.1:WP_193345603.1 156 DVLSHYKIAVGSTGNLGLSIGVMGAELGFKVTVHMSADAKGWKKALLRSKGVEVIEYTSDYSKAVEEGRRQAE 228 ************************************************************************* PP TIGR02035 221 adplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhv 293 +d ++f+dde+srdlflGyava+ rlk+ql+k ++kvd++hplfvylpcGvGGgpGGv+fGlk++f+++vh+ NCBI__GCF_000021925.1:WP_193345603.1 229 GDSRCHFIDDENSRDLFLGYAVAGLRLKEQLEKLNRKVDADHPLFVYLPCGVGGGPGGVTFGLKQVFQEHVHC 301 ************************************************************************* PP TIGR02035 294 ffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllal 366 ffaepthspcm+lGl tGlh+ i+vqdiG+dn+t+adGlavgr+s +vG+++ ll+G +tv+d +l++ll+ NCBI__GCF_000021925.1:WP_193345603.1 302 FFAEPTHSPCMVLGLATGLHDGIAVQDIGLDNKTEADGLAVGRASRFVGKIMAGLLSGAFTVEDAELFRLLQA 374 ************************************************************************* PP TIGR02035 367 laesedkrlepsalaglaGvvrllkeeeskreaek.liakklenavhlvwatGGkmvpeeemeayl 431 l++ e+++ epsalag+aG++rll +e+ +++++ + + l++ +hl+watGG++vpee m+ yl NCBI__GCF_000021925.1:WP_193345603.1 375 LDHAEGIQCEPSALAGMAGPARLLLCKEGLQYIREhRLEEGLKKGTHLIWATGGSLVPEEVMKDYL 440 *******************************9876156788**********************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (431 nodes) Target sequences: 1 (444 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: 17.04 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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