Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate BWI76_RS08740 BWI76_RS08740 histidine ammonia-lyase
Query= reanno::Koxy:BWI76_RS08740 (507 letters) >FitnessBrowser__Koxy:BWI76_RS08740 Length = 507 Score = 978 bits (2528), Expect = 0.0 Identities = 507/507 (100%), Positives = 507/507 (100%) Query: 1 MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF 60 MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF Sbjct: 1 MNALTLIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGF 60 Query: 61 GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI 120 GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI Sbjct: 61 GLLAQTRISTEDLENLQRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVI 120 Query: 121 QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA 180 QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA Sbjct: 121 QALIGLVNAGVTPWIPAKGSVGASGDLAPLAHMSLTLLGEGKARVRGGEWLPATEALRQA 180 Query: 181 GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP 240 GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP Sbjct: 181 GLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFSSAVVCGALTTEAALGSRRPFDP 240 Query: 241 RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ 300 RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ Sbjct: 241 RIHEARGQRGQIDAAALYRHLLTDDSAISQSHHNCTKVQDPYSLRCQPQVMGACLTQLRQ 300 Query: 301 AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360 AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL Sbjct: 301 AAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360 Query: 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS 420 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS Sbjct: 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVS 420 Query: 421 MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED 480 MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED Sbjct: 421 MAPAAGRRLWAMAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTED 480 Query: 481 RFFAPDIENAIALLAARHLTRLLPAVL 507 RFFAPDIENAIALLAARHLTRLLPAVL Sbjct: 481 RFFAPDIENAIALLAARHLTRLLPAVL 507 Lambda K H 0.318 0.132 0.374 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: 872 Number of extensions: 16 Number of successful extensions: 3 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: 507 Length of database: 507 Length adjustment: 34 Effective length of query: 473 Effective length of database: 473 Effective search space: 223729 Effective search space used: 223729 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 BWI76_RS08740 BWI76_RS08740 (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.29145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-219 714.8 3.6 2.9e-219 714.6 3.6 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS08740 BWI76_RS08740 histidine ammonia- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS08740 BWI76_RS08740 histidine ammonia-lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 714.6 3.6 2.9e-219 2.9e-219 3 499 .. 6 504 .. 4 507 .] 0.98 Alignments for each domain: == domain 1 score: 714.6 bits; conditional E-value: 2.9e-219 TIGR01225 3 ldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeL 73 l +++l+l++l+ v+ + +++l+++a +a++ s a++++i+ae +t YG+ntGFG la+++i +edl++L lcl|FitnessBrowser__Koxy:BWI76_RS08740 6 LIPGQLSLSQLRDVYSQPLKLALDESAFAAIDDSVACVNAILAEGRTAYGINTGFGLLAQTRISTEDLENL 76 667899***************************************************************** PP TIGR01225 74 qrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDL 144 qr+lv+sHaaGvGepl+++++R+++vl++nsl++G+sg+r v+++l+ l+na+v+P +p kGsvGasGDL lcl|FitnessBrowser__Koxy:BWI76_RS08740 77 QRSLVLSHAAGVGEPLDDDLARLIMVLKINSLSRGFSGIRLSVIQALIGLVNAGVTPWIPAKGSVGASGDL 147 *********************************************************************** PP TIGR01225 145 APLahlalvliGeGeae.fegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaeklle 214 APLah++l+l+GeG+a+ ge+++a+eaL++agleP+tl+akEGlAL+nGtq++ta+a+++l++ae+l + lcl|FitnessBrowser__Koxy:BWI76_RS08740 148 APLAHMSLTLLGEGKARvRGGEWLPATEALRQAGLEPITLAAKEGLALLNGTQASTAFALRGLFEAEDLFS 218 *****************55689************************************************* PP TIGR01225 215 sadiaaalsleallgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPq 284 sa +++al++ea+lg++++fdp+ihe+r++rgqi+ aa r+ll+ +s i++sh+++++vqD+YslRc+Pq lcl|FitnessBrowser__Koxy:BWI76_RS08740 219 SAVVCGALTTEAALGSRRPFDPRIHEARGQRGQIDAAALYRHLLTdDSAISQSHHNCTKVQDPYSLRCQPQ 289 *******************************************9989************************ PP TIGR01225 285 vhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRier 355 v+Ga+l++l+q++evl +E+n+++DnPlvfa e++v+sgGnFH+epvA+a+d++a+aiae+g++seRRi++ lcl|FitnessBrowser__Koxy:BWI76_RS08740 290 VMGACLTQLRQAAEVLLVEANAVSDNPLVFASENDVISGGNFHAEPVAMAADNIALAIAEIGSLSERRIAL 360 *********************************************************************** PP TIGR01225 356 lldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarklle 426 ++d ++s+LppFL++++G+nsG+miaq+taAaL+senkaL+hP+svDs+ptsanqEDHvsm+ aa+r+l+ lcl|FitnessBrowser__Koxy:BWI76_RS08740 361 MMDSHMSQLPPFLVKNGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGRRLWA 431 *********************************************************************** PP TIGR01225 427 vvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaa 497 ++en+r v+a+E+la++qgl++r+ ++++ le++++++Re v++++eDR++apD+e++ ll++++l+ lcl|FitnessBrowser__Koxy:BWI76_RS08740 432 MAENTRGVLAVEWLASVQGLDMREGLTSSPLLEEARHLLRERVTHYTEDRFFAPDIENAIALLAARHLTRL 502 ****************************************************************9999877 PP TIGR01225 498 ve 499 ++ lcl|FitnessBrowser__Koxy:BWI76_RS08740 503 LP 504 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (506 nodes) Target sequences: 1 (507 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.31 // [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