Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BWI76_RS22880 BWI76_RS22880 L-serine ammonia-lyase
Query= BRENDA::P30744 (455 letters) >FitnessBrowser__Koxy:BWI76_RS22880 Length = 455 Score = 827 bits (2135), Expect = 0.0 Identities = 412/455 (90%), Positives = 430/455 (94%) Query: 1 MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGH 60 MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLI R LL +VT+VVVDVYGSLSLTGKGH Sbjct: 1 MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIERGLLPEVTKVVVDVYGSLSLTGKGH 60 Query: 61 HTDIAIIMGLAGNLPDTVDIDSIPSFIQDVNTHGRLMLANGQHEVEFPVDQCMNFHADNL 120 HTDIAIIMGLAGNLPDTVDID+IP FIQDVNTHGRLMLANGQ EV FPVD+CMNFHADNL Sbjct: 61 HTDIAIIMGLAGNLPDTVDIDAIPGFIQDVNTHGRLMLANGQQEVAFPVDRCMNFHADNL 120 Query: 121 SLHENGMRITALAGDKVVYSQTYYSIGGGFIVDEEHFGQQDSAPVEVPYPYSSAADLQKH 180 S HENGMRITAL G+K++YSQTYYSIGGGFIVDE+HFG APV VPYPY +AADLQ+H Sbjct: 121 SRHENGMRITALGGEKILYSQTYYSIGGGFIVDEDHFGVTAEAPVAVPYPYKNAADLQRH 180 Query: 181 CQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVPRRA 240 C+E+GLSLSGLMM+NELALHSKE LEQH A VWEVM GIERGI+TEGVLPGKLRVPRRA Sbjct: 181 CRESGLSLSGLMMQNELALHSKEALEQHFAAVWEVMSSGIERGITTEGVLPGKLRVPRRA 240 Query: 241 AALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYY 300 AALRRMLVSQD T +DPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGI+PAVLAYY Sbjct: 241 AALRRMLVSQDNTNSDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300 Query: 301 DKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGA 360 DKFIR+VNANSLARY+LV SAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLG Sbjct: 301 DKFIRKVNANSLARYMLVTSAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360 Query: 361 SPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC 420 SP QVCIAAEI MEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC Sbjct: 361 SPGQVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC 420 Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD 455 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD Sbjct: 421 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD 455 Lambda K H 0.319 0.134 0.388 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: 711 Number of extensions: 17 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: 455 Length of database: 455 Length adjustment: 33 Effective length of query: 422 Effective length of database: 422 Effective search space: 178084 Effective search space used: 178084 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate BWI76_RS22880 BWI76_RS22880 (L-serine ammonia-lyase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))
# 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/TIGR00720.hmm # target sequence database: /tmp/gapView.16103.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00720 [M=450] Accession: TIGR00720 Description: sda_mono: L-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-223 726.1 1.3 1e-222 725.9 1.3 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS22880 BWI76_RS22880 L-serine ammonia-l Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS22880 BWI76_RS22880 L-serine ammonia-lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.9 1.3 1e-222 1e-222 1 450 [] 2 451 .. 2 451 .. 0.99 Alignments for each domain: == domain 1 score: 725.9 bits; conditional E-value: 1e-222 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleG 71 isvfd+fkiGiGPssshtvGPmka+k+f ++l ++g l +v++v vd+yGsl+ltGkGh+td a+++Gl+G lcl|FitnessBrowser__Koxy:BWI76_RS22880 2 ISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIERGLLPEVTKVVVDVYGSLSLTGKGHHTDIAIIMGLAG 72 79********************************************************************* PP TIGR00720 72 elpeevdiesieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkekt 141 +lp++vdi+ i+ ++++v+++++l la +q+e+ f +++ ++f+ ++l++heng+r++a+ +e ++l+++t lcl|FitnessBrowser__Koxy:BWI76_RS22880 73 NLPDTVDIDAIPGFIQDVNTHGRLMLAnGQQEVAFPVDRCMNFHADNLSRHENGMRITALGGE-KILYSQT 142 **************************97899******************************99.9****** PP TIGR00720 142 yysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiw 212 yys+GGGfivde++++ ++e + vpyp+k+aa+l ++C+e+gls+s ++++ne al+s+e+ +++++++w lcl|FitnessBrowser__Koxy:BWI76_RS22880 143 YYSIGGGFIVDEDHFGVTAEAPVAVPYPYKNAADLQRHCRESGLSLSGLMMQNELALHSKEALEQHFAAVW 213 *********************************************************************** PP TIGR00720 213 kvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvta 283 +vm++ ierg+++egvlpG l+v+rraa+l+r+l ++++t++dp+av+dw+n++alavneenaaGgrvvta lcl|FitnessBrowser__Koxy:BWI76_RS22880 214 EVMSSGIERGITTEGVLPGKLRVPRRAAALRRMLVSQDNTNSDPMAVVDWINMFALAVNEENAAGGRVVTA 284 *********************************************************************** PP TIGR00720 284 PtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaagla 354 PtnGa+gi+Pavlayy+kf+++++ +++ r++l+++aiG+lyk+nasisgaevGCqgevGvacsmaaagla lcl|FitnessBrowser__Koxy:BWI76_RS22880 285 PTNGACGIVPAVLAYYDKFIRKVNANSLARYMLVTSAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLA 355 *********************************************************************** PP TIGR00720 355 ellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvie 425 ellgg+p qv++aaei+mehnlGltCdPv+G+vq+PCiernaiaavka+naar+al+++++++v ldkvie lcl|FitnessBrowser__Koxy:BWI76_RS22880 356 ELLGGSPGQVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVCLDKVIE 426 *********************************************************************** PP TIGR00720 426 tmretGkdmkakyketskgGlavkv 450 tm+etGkdm+aky+ets+gGla+k+ lcl|FitnessBrowser__Koxy:BWI76_RS22880 427 TMYETGKDMNAKYRETSRGGLAMKI 451 **********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (450 nodes) Target sequences: 1 (455 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.96 // [ok]
This GapMind analysis is from Sep 17 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