Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_090448470.1 BLS63_RS24790 L-serine ammonia-lyase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5557 (458 letters) >NCBI__GCF_900100495.1:WP_090448470.1 Length = 458 Score = 815 bits (2106), Expect = 0.0 Identities = 408/458 (89%), Positives = 428/458 (93%) Query: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60 MSLSVFDLFKIGIGPSSSHTVGPMRAA RFAEGLRRDDLL TT +KVELYGSLGATGKG Sbjct: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAVRFAEGLRRDDLLAATTCIKVELYGSLGATGKG 60 Query: 61 HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKPL 120 HGSDKAVLLGLEGE PD+VDT T+DARL AIR+SG L LLGE I F EK HLAM+RKPL Sbjct: 61 HGSDKAVLLGLEGEQPDSVDTSTIDARLAAIRTSGELLLLGEKPIHFVEKEHLAMVRKPL 120 Query: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDL 180 +HPNGMIFRAFDAAGLQ+R+REYYSVGGGFVVDE AAGADRIVED TPL +PFKSAKDL Sbjct: 121 PYHPNGMIFRAFDAAGLQIRAREYYSVGGGFVVDEAAAGADRIVEDRTPLAYPFKSAKDL 180 Query: 181 LGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240 L HC+ + LSISQ+ML NE+AWRPE ETRAGLLKIWQVMQDCVAAGCR+EGI+PGGLKV+ Sbjct: 181 LAHCAEHQLSISQLMLANEAAWRPETETRAGLLKIWQVMQDCVAAGCRHEGIMPGGLKVR 240 Query: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300 RRAAAL+RQLC +PEAALRD LSVLDWVNLYALAVNEENA GGRVVTAPTNGAAGI+PAV Sbjct: 241 RRAAALYRQLCDHPEAALRDSLSVLDWVNLYALAVNEENASGGRVVTAPTNGAAGIVPAV 300 Query: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 LHYY RFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE Sbjct: 301 LHYYSRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 Query: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINA RMA+RGDG Sbjct: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAARMALRGDGQ 420 Query: 421 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458 HFVSLDKVIRTMRQTGADM SKYKETARGGLAVNIIEC Sbjct: 421 HFVSLDKVIRTMRQTGADMSSKYKETARGGLAVNIIEC 458 Lambda K H 0.320 0.136 0.401 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: 836 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: 458 Length of database: 458 Length adjustment: 33 Effective length of query: 425 Effective length of database: 425 Effective search space: 180625 Effective search space used: 180625 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 WP_090448470.1 BLS63_RS24790 (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.42212.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-222 725.7 0.1 1.3e-222 725.5 0.1 1.0 1 NCBI__GCF_900100495.1:WP_090448470.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100495.1:WP_090448470.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.5 0.1 1.3e-222 1.3e-222 2 450 .] 4 455 .. 3 455 .. 0.99 Alignments for each domain: == domain 1 score: 725.5 bits; conditional E-value: 1.3e-222 TIGR00720 2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 svfdlfkiGiGPssshtvGPm+aa +f+e l++ + l++++ +kv+lyGsl++tGkGh++dkavllGleGe+p NCBI__GCF_900100495.1:WP_090448470.1 4 SVFDLFKIGIGPSSSHTVGPMRAAVRFAEGLRRDDLLAATTCIKVELYGSLGATGKGHGSDKAVLLGLEGEQP 76 9************************************************************************ PP TIGR00720 75 eevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGG 147 ++vd+ +i+++l++++++++l l+++k i+f ++++la+ ++ lp+h+ng+ ++a+d +g ++++++yysvGG NCBI__GCF_900100495.1:WP_090448470.1 77 DSVDTSTIDARLAAIRTSGELLLLGEKPIHFVEKEHLAMVRKPLPYHPNGMIFRAFDAAGLQIRAREYYSVGG 149 ************************************************************************* PP TIGR00720 148 Gfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeec 218 Gf+vde++++ ++ e+ ++ypfksa++ll++C+e++lsis+++l+ne+a+r+e+e+ra ll+iw+vm++c NCBI__GCF_900100495.1:WP_090448470.1 150 GFVVDEAAAGADRIVEDrtPLAYPFKSAKDLLAHCAEHQLSISQLMLANEAAWRPETETRAGLLKIWQVMQDC 222 *******998887666545899*************************************************** PP TIGR00720 219 ierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaag 290 + g+++eg++pGglkv+rraa+l+r+l ++ e+ +d l+vldwvnlyalavneena+GgrvvtaPtnGaag NCBI__GCF_900100495.1:WP_090448470.1 223 VAAGCRHEGIMPGGLKVRRRAAALYRQLCDHPEAAlRDSLSVLDWVNLYALAVNEENASGGRVVTAPTNGAAG 295 ********************************9999************************************* PP TIGR00720 291 iiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeq 363 i+Pavl+yy++f++ ase+ vvrfllta+aiGilykenasisgaevGCqgevGvacsmaa++l+e+lgg+++q NCBI__GCF_900100495.1:WP_090448470.1 296 IVPAVLHYYSRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCEVLGGSVQQ 368 ************************************************************************* PP TIGR00720 364 venaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmka 436 venaaei+mehnlGltCdP+gGlvq+PCierna+++vkainaar+al++dg+++vsldkvi+tmr+tG+dm++ NCBI__GCF_900100495.1:WP_090448470.1 369 VENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAARMALRGDGQHFVSLDKVIRTMRQTGADMSS 441 ************************************************************************* PP TIGR00720 437 kyketskgGlavkv 450 kyket++gGlav++ NCBI__GCF_900100495.1:WP_090448470.1 442 KYKETARGGLAVNI 455 ************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (450 nodes) Target sequences: 1 (458 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: 27.33 // [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