Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate PfGW456L13_320 Histidine ammonia-lyase (EC 4.3.1.3)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_320 (510 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 Length = 510 Score = 978 bits (2528), Expect = 0.0 Identities = 510/510 (100%), Positives = 510/510 (100%) Query: 1 MTALNLIPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGF 60 MTALNLIPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGF Sbjct: 1 MTALNLIPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGF 60 Query: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRVVI 120 GLLASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRVVI Sbjct: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRVVI 120 Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180 Query: 181 LTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240 LTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR Sbjct: 181 LTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240 Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA 300 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA 300 Query: 301 AEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 AEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM Sbjct: 301 AEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420 Query: 421 APAAGKRLWEMAENTRGILAVEWLAAVQGLDLRNGLKTSPKLEKARAILRNEVPFYEKDR 480 APAAGKRLWEMAENTRGILAVEWLAAVQGLDLRNGLKTSPKLEKARAILRNEVPFYEKDR Sbjct: 421 APAAGKRLWEMAENTRGILAVEWLAAVQGLDLRNGLKTSPKLEKARAILRNEVPFYEKDR 480 Query: 481 FFAPDINAASELLASRCLNELVSAKLLPSL 510 FFAPDINAASELLASRCLNELVSAKLLPSL Sbjct: 481 FFAPDINAASELLASRCLNELVSAKLLPSL 510 Lambda K H 0.317 0.131 0.366 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: 12 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 PfGW456L13_320 (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.2829.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-224 730.1 4.7 6.5e-224 729.9 4.7 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 Histidine ammonia-lyase (EC 4.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 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 ! 729.9 4.7 6.5e-224 6.5e-224 4 504 .. 7 508 .. 4 510 .] 0.99 Alignments for each domain: == domain 1 score: 729.9 bits; conditional E-value: 6.5e-224 TIGR01225 4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGk 59 +++ltl++l+ v+++ +++l+++a++++++s a++e+i+ae++t YG+ntGFG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 7 IPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGFGL 62 5789**************************************************** PP TIGR01225 60 lasvkidkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvrae 115 las++i++edl++Lqr+lv+sHaaGvG+p+++e+vR+++vl++nsl++G+sg+r+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 63 LASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRV 118 ******************************************************** PP TIGR01225 116 vlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGeGeaefegevmdaae 171 v+++l+al+naev+P++p kGsvGasGDLAPLah++lvl+GeG+a+++ge+m+a+e lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 119 VIDALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATE 174 ******************************************************** PP TIGR01225 172 aLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleal 227 aL+ agl P+tl+akEGlAL+nGtq++ta+a+++l++ e+l + a + ++l++ea+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 175 ALKVAGLTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAV 230 ******************************************************** PP TIGR01225 228 lgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRci 282 lg++++fd++ih++r+++gqi+ aa+ r+ll se+++sh+++++vqD+YslRc+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 231 LGSRSPFDARIHAARGQKGQIDAAAAYRDLLGeRSEVSDSHENCEKVQDPYSLRCQ 286 *******************************978********************** PP TIGR01225 283 PqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldfl 338 Pqv+Ga+l++++q++evlaiE n+++DnPlvfa+eg+v+sgGnFH+epvA+a+d++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 287 PQVMGACLTQFRQAAEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNM 342 ******************************************************** PP TIGR01225 339 aiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenka 394 a+aiae+g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taAaL+senka lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 343 ALAIAEIGSLSERRISLMMDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKA 398 ******************************************************** PP TIGR01225 395 LahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrk 450 L+hP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r ++a+E+laa+qgl++r+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 399 LSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGILAVEWLAAVQGLDLRN 454 ******************************************************** PP TIGR01225 451 aektaaelekvyeavRevveeleeDRvlapDleavkellekesleaaveakvka 504 kt+++lek+++ +R++v+ +e+DR++apD++a++ell+++ l++ v+ak+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_320 455 GLKTSPKLEKARAILRNEVPFYEKDRFFAPDINAASELLASRCLNELVSAKLLP 508 *********************************************999988766 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.27 // [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