Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate PfGW456L13_321 Histidine ammonia-lyase (EC 4.3.1.3)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1582 (507 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 Length = 507 Score = 910 bits (2352), Expect = 0.0 Identities = 462/507 (91%), Positives = 484/507 (95%) Query: 1 MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60 MSQAEKIVI ++ + WQDVVAVARHGAQLELS IW RIENAQAIVQRIV SGERAYG+N Sbjct: 1 MSQAEKIVITESQVSWQDVVAVARHGAQLELSAPIWARIENAQAIVQRIVTSGERAYGIN 60 Query: 61 TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120 TGLGALCNVSL+ EQLSQLSRNTLLSHACGVG PL DEQTR+I+CAAI NYSHGKSG+HR Sbjct: 61 TGLGALCNVSLQDEQLSQLSRNTLLSHACGVGVPLTDEQTRSIMCAAIVNYSHGKSGLHR 120 Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180 +VVEALLALLNRGITPQVPSQGSVGYLTHMAHIGI LLGVGNVSYRGQIV+AQQAL+EEG Sbjct: 121 QVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGNVSYRGQIVSAQQALAEEG 180 Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240 LQPV+LGAKDGLCLVNGTPCM+GLSCLAIADATRL++WADVIGAMSFEAQRGQI AFDAE Sbjct: 181 LQPVKLGAKDGLCLVNGTPCMSGLSCLAIADATRLLEWADVIGAMSFEAQRGQIDAFDAE 240 Query: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300 IIALKPH GMQQVGINLRALLDGSEVIA SKGIRTQDALSIRSIPQVHGAARDQL HA K Sbjct: 241 IIALKPHPGMQQVGINLRALLDGSEVIAQSKGIRTQDALSIRSIPQVHGAARDQLVHAIK 300 Query: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360 QIETELN TDNP++LGT DN+RV+SQANPHGQSVA+AADLLAIAMAEIGSIAERRLDRL Sbjct: 301 QIETELNGATDNPLVLGTADNYRVVSQANPHGQSVAMAADLLAIAMAEIGSIAERRLDRL 360 Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLS+ Sbjct: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSL 420 Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480 Query: 481 WLAPDIAAAAGVLKDPILLHKALPNLN 507 WLAPDIAAAA VLKDP+LL K LPNLN Sbjct: 481 WLAPDIAAAASVLKDPVLLQKTLPNLN 507 Lambda K H 0.319 0.133 0.384 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: 953 Number of extensions: 27 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 PfGW456L13_321 (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.10896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-166 540.2 6.9 2.6e-166 539.9 6.9 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 Histidine ammonia-lyase (EC 4.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 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 ! 539.9 6.9 2.6e-166 2.6e-166 1 495 [. 7 499 .. 7 505 .. 0.98 Alignments for each domain: == domain 1 score: 539.9 bits; conditional E-value: 2.6e-166 TIGR01225 1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntG 56 +v+ +++++ +d++avar++a++elsa +++++++a++++iv++ + YG+ntG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 7 IVITESQVSWQDVVAVARHGAQLELSAPIWARIENAQAIVQRIVTSGERAYGINTG 62 6889999************************************************* PP TIGR01225 57 FGklasvkidkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgv 112 G+l +v ++ e+l +L rn ++sHa+GvG pl++e +R ++ + ++G sg+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 63 LGALCNVSLQDEQLSQLSRNTLLSHACGVGVPLTDEQTRSIMCAAIVNYSHGKSGL 118 ******************************************************** PP TIGR01225 113 raevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGeGeaefegevmd 168 ++v+e+l+alln++++P vp++GsvG L +ah++++l+G G++ ++g++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 119 HRQVVEALLALLNRGITPQVPSQGSVG---YLTHMAHIGIALLGVGNVSYRGQIVS 171 **************************7...6999********************** PP TIGR01225 169 aaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsl 224 a++aLa+ gl+Pv+l ak+Gl L+nGt +m++l +la++da +lle ad+++a+s+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 172 AQQALAEEGLQPVKLGAKDGLCLVNGTPCMSGLSCLAIADATRLLEWADVIGAMSF 227 ******************************************************** PP TIGR01225 225 eallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslR 280 ea g +afd++i +++ph+g +v+ +lr ll+gse+ + + r qDa s+R lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 228 EAQRGQIDAFDAEIIALKPHPGMQQVGINLRALLDGSEVIAQS-KGIRTQDALSIR 282 ***************************************9998.678********* PP TIGR01225 281 ciPqvhGavldtldqvkevlaiElnsatDnPlvf..adegevvsgGnFHgepvAla 334 +iPqvhGa++d+l ++ + +++Eln atDnPlv+ ad+ +vvs n Hg+ vA+a lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 283 SIPQVHGAARDQLVHAIKQIETELNGATDNPLVLgtADNYRVVSQANPHGQSVAMA 338 *********************************83356789*************** PP TIGR01225 335 ldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvs 390 +d laia+ae+g+i+eRR++rl++p+ s+Lp+FL++++G+nsG+mi qy aA+L+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 339 ADLLAIAMAEIGSIAERRLDRLINPHVSGLPAFLVANPGVNSGMMIVQYVAASLCA 394 ******************************************************** PP TIGR01225 391 enkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqgl 446 en++La+Pa +D+ ts+ qEDH s+g+ aa kl ++ en ++++aiE+l+aaq+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 395 ENRQLAQPAVLDNYVTSGLQEDHLSLGTNAALKLHRALENCTQILAIEYLLAAQAF 450 ******************************************************** PP TIGR01225 447 efrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesle 495 ef+k+++ a ++ + ++Re v+ +++DR lapD++a+ ++l++ +l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 451 EFLKEQRFGAGTDTAWRLLRERVPAYDQDRWLAPDIAAAASVLKDPVLL 499 ****************************************999987665 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: 00:00:00.03 # Mc/sec: 8.24 // [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