Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BWI76_RS17875 BWI76_RS17875 L-serine ammonia-lyase
Query= BRENDA::P16095 (454 letters) >FitnessBrowser__Koxy:BWI76_RS17875 Length = 454 Score = 823 bits (2125), Expect = 0.0 Identities = 400/454 (88%), Positives = 436/454 (96%) Query: 1 MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60 MIS+FDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLL+ VTR+AVDVYGSLSLTGKGH Sbjct: 1 MISIFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLNEVTRLAVDVYGSLSLTGKGH 60 Query: 61 HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL 120 HTDIAIIMGLAGN+P TVDID+IP FIRDVEER RLLLAQG+HEVDFP+++GMRF + NL Sbjct: 61 HTDIAIIMGLAGNQPDTVDIDAIPAFIRDVEERGRLLLAQGQHEVDFPKNDGMRFRSDNL 120 Query: 121 PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY 180 PLHENGM IHA++G++ +YSKTYYSIGGGFIVDEEHFG+++A+E++VPYPFKSA E+L Y Sbjct: 121 PLHENGMTIHAWSGEKEIYSKTYYSIGGGFIVDEEHFGKESASELAVPYPFKSAQEMLGY 180 Query: 181 CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA 240 C +TG SLSG+ MQNELALHSKKEI++YFA++WQTM+ACIDRGMNTEGVLPGPLRVPRRA Sbjct: 181 CKQTGMSLSGMVMQNELALHSKKEIEDYFANIWQTMRACIDRGMNTEGVLPGPLRVPRRA 240 Query: 241 SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300 SALRRMLV+SDKLSNDPMNV+DWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY Sbjct: 241 SALRRMLVASDKLSNDPMNVVDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300 Query: 301 DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360 DHFIE VSPDIY RYF+A+GAIG LYKMNASISGAEVGCQGEVGVACSMAAAGLAE+LG Sbjct: 301 DHFIEPVSPDIYIRYFLASGAIGTLYKMNASISGAEVGCQGEVGVACSMAAAGLAEILGA 360 Query: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS 420 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINA+RMA+RRTS PRVS Sbjct: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINASRMAMRRTSEPRVS 420 Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD 454 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD Sbjct: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD 454 Lambda K H 0.318 0.135 0.396 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: 780 Number of extensions: 22 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: 454 Length of database: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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 BWI76_RS17875 BWI76_RS17875 (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.30253.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-232 756.6 0.1 5.4e-232 756.4 0.1 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS17875 BWI76_RS17875 L-serine ammonia-l Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS17875 BWI76_RS17875 L-serine ammonia-lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 756.4 0.1 5.4e-232 5.4e-232 1 450 [] 2 451 .. 2 451 .. 0.99 Alignments for each domain: == domain 1 score: 756.4 bits; conditional E-value: 5.4e-232 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleG 71 is+fd+fk+GiGPssshtvGPmka+k+fv++l +kg l++v+r++vd+yGsl+ltGkGh+td a+++Gl+G lcl|FitnessBrowser__Koxy:BWI76_RS17875 2 ISIFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLNEVTRLAVDVYGSLSLTGKGHHTDIAIIMGLAG 72 79********************************************************************* PP TIGR00720 72 elpeevdiesieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkekt 141 ++p++vdi+ i++++++vee+++l la +q+e++f +++ ++f++++lplheng++++a+++e + +++kt lcl|FitnessBrowser__Koxy:BWI76_RS17875 73 NQPDTVDIDAIPAFIRDVEERGRLLLAqGQHEVDFPKNDGMRFRSDNLPLHENGMTIHAWSGE-KEIYSKT 142 **************************9789*******************************99.889**** PP TIGR00720 142 yysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiw 212 yys+GGGfivdee+++ke+++e vpypfksa+e+l +Ck++g+s+s +v++ne al+s++e+++++++iw lcl|FitnessBrowser__Koxy:BWI76_RS17875 143 YYSIGGGFIVDEEHFGKESASELAVPYPFKSAQEMLGYCKQTGMSLSGMVMQNELALHSKKEIEDYFANIW 213 *********************************************************************** PP TIGR00720 213 kvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvta 283 ++m++ci+rg+++egvlpG+l+v+rra++l+r+l a+++ s+dp++v+dwvn++alavneenaaGgrvvta lcl|FitnessBrowser__Koxy:BWI76_RS17875 214 QTMRACIDRGMNTEGVLPGPLRVPRRASALRRMLVASDKLSNDPMNVVDWVNMFALAVNEENAAGGRVVTA 284 *********************************************************************** PP TIGR00720 284 PtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaagla 354 PtnGa+gi+Pavlayy++f+e +s ++++r++l++gaiG+lyk+nasisgaevGCqgevGvacsmaaagla lcl|FitnessBrowser__Koxy:BWI76_RS17875 285 PTNGACGIVPAVLAYYDHFIEPVSPDIYIRYFLASGAIGTLYKMNASISGAEVGCQGEVGVACSMAAAGLA 355 *********************************************************************** PP TIGR00720 355 ellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvie 425 e+lg++peqv++aaei+mehnlGltCdPv+G+vq+PCiernaia+vkaina+r+a++++++++vsldkvie lcl|FitnessBrowser__Koxy:BWI76_RS17875 356 EILGASPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINASRMAMRRTSEPRVSLDKVIE 426 *********************************************************************** PP TIGR00720 426 tmretGkdmkakyketskgGlavkv 450 tm+etGkdm+aky+ets+gGla+kv lcl|FitnessBrowser__Koxy:BWI76_RS17875 427 TMYETGKDMNAKYRETSRGGLAIKV 451 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (450 nodes) Target sequences: 1 (454 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: 10.55 // [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