Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Pf6N2E2_3800 Histidine ammonia-lyase (EC 4.3.1.3)
Query= reanno::pseudo5_N2C3_1:AO356_09605 (507 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 Length = 507 Score = 954 bits (2467), Expect = 0.0 Identities = 489/507 (96%), Positives = 496/507 (97%) Query: 1 MSQAEKIVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVN 60 MSQAEKIVI APLRWQDVVAVARFGAELELS Q WARIDNAQAIVQRIVESGERAYGVN Sbjct: 1 MSQAEKIVIADAPLRWQDVVAVARFGAELELSAQAWARIDNAQAIVQRIVESGERAYGVN 60 Query: 61 TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHR 120 TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPL+DEQTRAI+CAAILNYSQGKSGIHR Sbjct: 61 TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPLSDEQTRAIICAAILNYSQGKSGIHR 120 Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEG 180 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHI IALLGVGQVSYRGQI+PAQQAL AEG Sbjct: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHISIALLGVGQVSYRGQIMPAQQALAAEG 180 Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240 LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE Sbjct: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240 Query: 241 IIALKPHPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQ 300 IIALKPHPGMQQVGVNLRALLDGSEVIA+S GIRTQDALSIRSIPQVHGAARDQLAHARQ Sbjct: 241 IIALKPHPGMQQVGVNLRALLDGSEVIASSLGIRTQDALSIRSIPQVHGAARDQLAHARQ 300 Query: 301 QIETELNAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360 QIETELNA TDNPLLLGTPE+FRVMSQANPHGQSVA+AADLLAIAMAEIGSIAERRLDRL Sbjct: 301 QIETELNAATDNPLLLGTPEHFRVMSQANPHGQSVAMAADLLAIAMAEIGSIAERRLDRL 360 Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM 420 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM Sbjct: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM 420 Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDR 480 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFG GTDIAWKLLRERVP YDQDR Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGTGTDIAWKLLRERVPAYDQDR 480 Query: 481 WLAPDIASAAGLLKDPNVLHNVLPNLN 507 WLAPDIASAAGLLKDP+VLH VLPNLN Sbjct: 481 WLAPDIASAAGLLKDPSVLHRVLPNLN 507 Lambda K H 0.320 0.133 0.385 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: 981 Number of extensions: 23 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: 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
Align candidate Pf6N2E2_3800 (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.8838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-170 552.2 6.4 5.8e-170 552.0 6.4 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 Histidine ammonia-lyase (EC 4.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 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 ! 552.0 6.4 5.8e-170 5.8e-170 2 494 .. 8 498 .. 7 505 .. 0.97 Alignments for each domain: == domain 1 score: 552.0 bits; conditional E-value: 5.8e-170 TIGR01225 2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvki 65 v+ l+ +d++avar +a++elsa+a +++++++a++++iv++ + YGvntG G+l +v + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 8 VIADAPLRWQDVVAVARFGAELELSAQAWARIDNAQAIVQRIVESGERAYGVNTGLGALCNVSL 71 667778999******************************************************* PP TIGR01225 66 dkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevl 129 + e+l +L rn ++sHa+GvG+pl++e +Ra++ + ++G sg+ ++v+e+l+alln++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 72 KDEQLSQLSRNTLLSHACGVGAPLSDEQTRAIICAAILNYSQGKSGIHRRVVEALLALLNRGIT 135 **************************************************************** PP TIGR01225 130 PvvpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALin 193 P vp++GsvG L +ah++++l+G G++ ++g++m+a++aLaa gl+Pv+l ak+Gl L+n lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 136 PQVPSQGSVG---YLTHMAHISIALLGVGQVSYRGQIMPAQQALAAEGLQPVQLGAKDGLCLVN 196 *********7...6999*********************************************** PP TIGR01225 194 Gtqlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrel 257 Gt +mt+l +lal+da +l++ ad+++a+s+ea g +afd++i +++ph+g +v+ +lr l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 197 GTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAEIIALKPHPGMQQVGVNLRAL 260 **************************************************************** PP TIGR01225 258 lagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvf..adege 319 l+gse+ s r qDa s+R+iPqvhGa++d+l+++++ +++Eln+atDnPl++ +++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 261 LDGSEVIASS-LGIRTQDALSIRSIPQVHGAARDQLAHARQQIETELNAATDNPLLLgtPEHFR 323 *********9.6789*****************************************83346689 PP TIGR01225 320 vvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqy 383 v+s n Hg+ vA+a+d laia+ae+g+i+eRR++rl++p+ s+Lp+FL++++G+nsG+mi qy lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 324 VMSQANPHGQSVAMAADLLAIAMAEIGSIAERRLDRLINPHVSGLPAFLVANPGVNSGMMIVQY 387 **************************************************************** PP TIGR01225 384 taAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqgle 447 aA+L+ enk+La+Pa +D+ ts+ qEDH smg+ aa kl ++ en ++++aiE+l+aaq+ e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 388 VAASLCAENKQLAQPAVLDNFVTSGLQEDHLSMGTNAALKLHRALENCTQILAIEYLLAAQAFE 451 **************************************************************** PP TIGR01225 448 frkaektaaelekvyeavRevveeleeDRvlapDleavkellekesl 494 f+ka++ + ++ + +++Re v+ +++DR lapD++ + ll++ s+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3800 452 FLKAQRFGTGTDIAWKLLRERVPAYDQDRWLAPDIASAAGLLKDPSV 498 ***************************************99987665 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9.53 // [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