Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Pf6N2E2_3799 Histidine ammonia-lyase (EC 4.3.1.3)
Query= reanno::pseudo6_N2E2:Pf6N2E2_3799 (510 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 Length = 510 Score = 978 bits (2528), Expect = 0.0 Identities = 510/510 (100%), Positives = 510/510 (100%) Query: 1 MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60 MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF Sbjct: 1 MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60 Query: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI Sbjct: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120 Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180 Query: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR Sbjct: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240 Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300 Query: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM Sbjct: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420 Query: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR Sbjct: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480 Query: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510 FFAPDINAASELLASRCLNELVTAQLLPSL Sbjct: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510 Lambda K H 0.318 0.132 0.370 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: 899 Number of extensions: 8 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 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: 52 (24.6 bits)
Align candidate Pf6N2E2_3799 (Histidine ammonia-lyase (EC 4.3.1.3))
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))
# 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/TIGR01225.hmm # target sequence database: /tmp/gapView.5216.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01225 [M=506] Accession: TIGR01225 Description: hutH: histidine 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-222 724.0 5.0 4.7e-222 723.8 5.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 Histidine ammonia-lyase (EC 4.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 Histidine ammonia-lyase (EC 4.3.1.3) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 723.8 5.0 4.7e-222 4.7e-222 4 504 .. 7 508 .. 4 510 .] 0.99 Alignments for each domain: == domain 1 score: 723.8 bits; conditional E-value: 4.7e-222 TIGR01225 4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidk 67 +++l+l++l+ ++++ ++l+a+a++++++s a++e+i+ae++t YG+ntGFG las++i++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 7 IPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGFGLLASTRIAS 70 567999********************************************************** PP TIGR01225 68 edlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPv 131 edl++Lqr+lv+sHaaGvGep+++++vR+++vl++nsl++G+sg+r++v+++l+al+naev+P+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 71 EDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVIDALIALINAEVYPH 134 **************************************************************** PP TIGR01225 132 vpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGt 195 +p kGsvGasGDLAPLah++lvl+GeG+a+++ge+++a eaL+ agl+P+tl+akEGlAL+nGt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 135 IPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAGLAPLTLAAKEGLALLNGT 198 **************************************************************** PP TIGR01225 196 qlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrella 259 q++ta+a+++l++ e+l + a + ++l++ea+lg++++fd++ih++r+++gqi+ aa+ r+ll lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 199 QVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDARIHAARGQKGQIDAAAAYRDLLG 262 ***************************************************************9 PP TIGR01225 260 .gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvs 322 se+++sh+++d+vqD+YslRc+Pqv+Ga+l++++q++evl iE+n+++DnPlvfa+eg+v+s lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 263 eRSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQAAEVLVIEANAVSDNPLVFAAEGDVIS 326 78************************************************************** PP TIGR01225 323 gGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaA 386 gGnFH+epvA+a+d++a+aiae+g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taA lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 327 GGNFHAEPVAMAADNMALAIAEIGSLSERRISLMMDKHMSQLPPFLVANGGVNSGFMIAQVTAA 390 **************************************************************** PP TIGR01225 387 aLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrk 450 aL+senkaL+hP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r ++a+E+laa+qgl++r lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 391 ALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGILAVEWLAACQGLDLRG 454 **************************************************************** PP TIGR01225 451 aektaaelekvyeavRevveeleeDRvlapDleavkellekesleaaveakvka 504 kt+++le+++ ++R++v+ +e+DR++apD++a++ell+++ l++ v+a++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 455 GLKTSTKLERARGLLRAQVPFYEKDRFFAPDINAASELLASRCLNELVTAQLLP 508 ********************************************9999887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (506 nodes) Target sequences: 1 (510 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.52 // [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