Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate GFF343 PS417_01750 histidine ammonia-lyase
Query= reanno::pseudo6_N2E2:Pf6N2E2_3799 (510 letters) >FitnessBrowser__WCS417:GFF343 Length = 510 Score = 924 bits (2389), Expect = 0.0 Identities = 480/510 (94%), Positives = 492/510 (96%) Query: 1 MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60 MTALNLIPGQLSLAQLR IYQQPVTLSLD SA+AQIEASVACVEQILAENRTAYGINTGF Sbjct: 1 MTALNLIPGQLSLAQLRAIYQQPVTLSLDDSATAQIEASVACVEQILAENRTAYGINTGF 60 Query: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI Sbjct: 61 GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120 Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWL A EALKVAG Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLEATEALKVAG 180 Query: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240 L PLTLAAKEGLALLNGTQVSTA+ALRGLFEGEDLFAGALA G LTVEAVLGSRSPFDAR Sbjct: 181 LTPLTLAAKEGLALLNGTQVSTAYALRGLFEGEDLFAGALACGALTVEAVLGSRSPFDAR 240 Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300 IHAARGQ+GQID+AAAYR LLGE S+VS SHQNCDKVQDPYSLRCQPQVMGACLTQFRQA Sbjct: 241 IHAARGQRGQIDSAAAYRHLLGESSQVSQSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300 Query: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 AEVLV+EANAVSDNPLVFAA+GDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM Sbjct: 301 AEVLVVEANAVSDNPLVFAAQGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360 Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420 MDKHMSQLPPFLV NGGVNSGFMIAQVTAAALASENKAL+HPHSVDSLPTSANQEDHVSM Sbjct: 361 MDKHMSQLPPFLVGNGGVNSGFMIAQVTAAALASENKALAHPHSVDSLPTSANQEDHVSM 420 Query: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480 APAAGKRLWEMAENTRG+LAVEWLAACQGLDLR GLKTS LE+ARG+LR +V FYEKDR Sbjct: 421 APAAGKRLWEMAENTRGVLAVEWLAACQGLDLREGLKTSPALEKARGILRGKVAFYEKDR 480 Query: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510 FFAPDINAASELLASRCLNELV A LLPSL Sbjct: 481 FFAPDINAASELLASRCLNELVPANLLPSL 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: 842 Number of extensions: 10 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 GFF343 PS417_01750 (histidine ammonia-lyase)
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.23450.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-224 729.9 5.4 7.3e-224 729.8 5.4 1.0 1 lcl|FitnessBrowser__WCS417:GFF343 PS417_01750 histidine ammonia-ly Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF343 PS417_01750 histidine ammonia-lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 729.8 5.4 7.3e-224 7.3e-224 4 504 .. 7 508 .. 4 510 .] 0.99 Alignments for each domain: == domain 1 score: 729.8 bits; conditional E-value: 7.3e-224 TIGR01225 4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlvr 79 +++l+l++l+a++++ ++l+++a++++++s a++e+i+ae++t YG+ntGFG las++i++edl++Lqr+lv+ lcl|FitnessBrowser__WCS417:GFF343 7 IPGQLSLAQLRAIYQQPVTLSLDDSATAQIEASVACVEQILAENRTAYGINTGFGLLASTRIASEDLENLQRSLVL 82 56799*********************************************************************** PP TIGR01225 80 sHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvli 155 sHaaGvGep+++++vR+++vl++nsl++G+sg+r++v+++l+al+naev+P++p kGsvGasGDLAPLah++lvl+ lcl|FitnessBrowser__WCS417:GFF343 83 SHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVIDALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLL 158 **************************************************************************** PP TIGR01225 156 GeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallgts 231 GeG+a+++ge+++a+eaL+ agl P+tl+akEGlAL+nGtq++ta+a+++l++ e+l + a +++al++ea+lg++ lcl|FitnessBrowser__WCS417:GFF343 159 GEGKARYKGEWLEATEALKVAGLTPLTLAAKEGLALLNGTQVSTAYALRGLFEGEDLFAGALACGALTVEAVLGSR 234 **************************************************************************** PP TIGR01225 232 kafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElns 306 ++fd++ih++r++rgqi++aa+ r+ll +s++++sh+++d+vqD+YslRc+Pqv+Ga+l++++q++evl +E+n+ lcl|FitnessBrowser__WCS417:GFF343 235 SPFDARIHAARGQRGQIDSAAAYRHLLGeSSQVSQSHQNCDKVQDPYSLRCQPQVMGACLTQFRQAAEVLVVEANA 310 ***************************97899******************************************** PP TIGR01225 307 atDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaq 382 ++DnPlvfa++g+v+sgGnFH+epvA+a+d++a+aiae+g++seRRi++++d+++s+LppFL+ ++G+nsG+miaq lcl|FitnessBrowser__WCS417:GFF343 311 VSDNPLVFAAQGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLMMDKHMSQLPPFLVGNGGVNSGFMIAQ 386 **************************************************************************** PP TIGR01225 383 ytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaael 458 +taAaL+senkaLahP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r v+a+E+laa+qgl++r+ kt+++l lcl|FitnessBrowser__WCS417:GFF343 387 VTAAALASENKALAHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAVEWLAACQGLDLREGLKTSPAL 462 **************************************************************************** PP TIGR01225 459 ekvyeavRevveeleeDRvlapDleavkellekesleaaveakvka 504 ek++ +R +v+ +e+DR++apD++a++ell+++ l++ v+a++++ lcl|FitnessBrowser__WCS417:GFF343 463 EKARGILRGKVAFYEKDRFFAPDINAASELLASRCLNELVPANLLP 508 *************************************999988765 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: 10.99 // [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