Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_051999841.1 L248_RS03260 D-serine ammonia-lyase
Query= BRENDA::Q4A041 (433 letters) >NCBI__GCF_000469325.1:WP_051999841.1 Length = 451 Score = 454 bits (1167), Expect = e-132 Identities = 226/432 (52%), Positives = 295/432 (68%), Gaps = 1/432 (0%) Query: 3 DLATLKQDFPLIDSMQNYKPIFWENPNFRKPASL-TFTLKDMEDAAQRLERFSSYISTVF 61 D L FP + + N P FW NP++ P + D+ DA R RF+ Y++ VF Sbjct: 13 DKQELLTQFPALAAYANETPTFWANPHYGHPRKDDSMREADVFDAGTRFRRFAPYLAEVF 72 Query: 62 PETENNHGLIESPLKHIPFMQNTLTNIESLPIEGKLWLKCDSHLAISGSIKARGGIYEVL 121 PET HG+IESP+ +P ++ + GKL++K DS L +SGSIK+RGGIYEVL Sbjct: 73 PETAPAHGIIESPIYRLPHLEKQIAADTGTVFPGKLFMKADSELPVSGSIKSRGGIYEVL 132 Query: 122 KLAETIAMQDGDLKETADYRVLAEQKYQDLFSKYNVAVGSTGNLGLSIGIMSAKLGFKVT 181 K AETIAM++GDL T DYR+L +Y+ LFSKY +AVGSTGNLGLSIGIM+A LGF+ T Sbjct: 133 KFAETIAMREGDLAYTDDYRILDSPRYKRLFSKYEIAVGSTGNLGLSIGIMAATLGFRTT 192 Query: 182 VHMSTDARQWKKDLLRSRGVEVIEHQSDYQYAVAEGRKHAENDPTCHFVDDEGSSDLFLG 241 VHMS DARQWKKD LR+ GV V+E+ +D+ A+ GRK AE+ P +F+DDEGS DLF G Sbjct: 193 VHMSADARQWKKDKLRANGVNVVEYDADFTTAITAGRKLAESQPNTYFIDDEGSKDLFFG 252 Query: 242 YTVAALRLKAQLAAENIQIDAEHPLFVYIPCGVGGGPGGVTFGLKQVFGEHVYCIFTEPT 301 Y VAA+RL QL I++DA+HP+FVY+P GVGG PGGVTFGLK V G +++ IF EPT Sbjct: 253 YAVAAIRLGKQLKDAGIKMDADHPVFVYLPAGVGGSPGGVTFGLKTVLGPNIHGIFAEPT 312 Query: 302 HAPCMLLGMMTQLHDKISVKDIGIDGNTDADGLAVARPSRLVGQIMNTLLYGIQTVSDSE 361 H P + +GM++ L +KI+V D+GIDG T ADGLAV RPSRL G++M+TLL G T D + Sbjct: 313 HMPSVTIGMISGLQEKITVYDLGIDGKTAADGLAVPRPSRLAGRVMDTLLLGSCTFPDHD 372 Query: 362 MYRYLYLLSEKEDIFIEPSAASGFAGIKSAITLAKQQGIQMNQANHIVWATGGNMVPKEE 421 M R+ L+E+E +EPS A G A ++ + K+ G + A HI+WATGG+MVP E Sbjct: 373 MMRWTARLAEQEQHNVEPSGAGGLAILERSFPALKKLGYPVENATHIIWATGGSMVPAPE 432 Query: 422 MLKYVNHGKSCL 433 M Y+ G + L Sbjct: 433 MADYIKTGDALL 444 Lambda K H 0.318 0.135 0.398 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: 503 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: 433 Length of database: 451 Length adjustment: 32 Effective length of query: 401 Effective length of database: 419 Effective search space: 168019 Effective search space used: 168019 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: 51 (24.3 bits)
Align candidate WP_051999841.1 L248_RS03260 (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.2760598.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-165 537.5 0.0 1.3e-165 537.3 0.0 1.0 1 NCBI__GCF_000469325.1:WP_051999841.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000469325.1:WP_051999841.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 537.3 0.0 1.3e-165 1.3e-165 2 430 .. 18 436 .. 17 437 .. 0.97 Alignments for each domain: == domain 1 score: 537.3 bits; conditional E-value: 1.3e-165 TIGR02035 2 llkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiieselv 74 l ++p ++ + +++wanp+ + k+ +++e++v +a r++rfapy+a+vfpeta ++Giies++ NCBI__GCF_000469325.1:WP_051999841.1 18 LTQFPALAAYANETPTFWANPHYG---HPRKDDSMREADVFDAGTRFRRFAPYLAEVFPETAPAHGIIESPIY 87 7899*****************865...8899999*************************************** PP TIGR02035 75 evaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklaeeefk 147 + +l+k++ ++ + ++G+l++k ds+lp+sGsik+rGGiyevlk+ae +a+++G l +ddy++l ++++k NCBI__GCF_000469325.1:WP_051999841.1 88 RLPHLEKQIAADTGTVFPGKLFMKADSELPVSGSIKSRGGIYEVLKFAETIAMREGDLAYTDDYRILDSPRYK 160 ************************************************************************* PP TIGR02035 148 dffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeae 220 +fs+y+iavGstGnlGlsiGi++a+lGf+ tvhmsada++wkkdklr++Gv+vvey++d+++a+ Grk ae NCBI__GCF_000469325.1:WP_051999841.1 161 RLFSKYEIAVGSTGNLGLSIGIMAATLGFRTTVHMSADARQWKKDKLRANGVNVVEYDADFTTAITAGRKLAE 233 ************************************************************************* PP TIGR02035 221 adplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhv 293 ++p++yf+dde s+dlf+Gyavaa rl kql+ +gik+d++hp+fvylp GvGG+pGGv+fGlk + g ++h NCBI__GCF_000469325.1:WP_051999841.1 234 SQPNTYFIDDEGSKDLFFGYAVAAIRLGKQLKDAGIKMDADHPVFVYLPAGVGGSPGGVTFGLKTVLGPNIHG 306 ************************************************************************* PP TIGR02035 294 ffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllal 366 +faepth p + +G+ +Gl eki+v+d+Gid++taadGlav rps l Gr+++ ll G t d+++ + a NCBI__GCF_000469325.1:WP_051999841.1 307 IFAEPTHMPSVTIGMISGLQEKITVYDLGIDGKTAADGLAVPRPSRLAGRVMDTLLLGSCTFPDHDMMRWTAR 379 ************************************************************************* PP TIGR02035 367 laesedkrlepsalaglaGvvrllkeeeskreaekliakklenavhlvwatGGkmvpeeemeay 430 lae+e+ +eps gla + r + +kl + +ena+h++watGG+mvp em+ y NCBI__GCF_000469325.1:WP_051999841.1 380 LAEQEQHNVEPSGAGGLAILERSF------PALKKL-GYPVENATHIIWATGGSMVPAPEMADY 436 ************877766544444......344444.779*********************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (431 nodes) Target sequences: 1 (451 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 21.62 // [ok]
This GapMind analysis is from Sep 24 2021. 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