Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate PfGW456L13_4961 Fumarylacetoacetase (EC 3.7.1.2)
Query= BRENDA::Q8RW90 (421 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 Length = 434 Score = 373 bits (957), Expect = e-108 Identities = 196/416 (47%), Positives = 262/416 (62%), Gaps = 14/416 (3%) Query: 16 FPIQNLPYGVFKPESNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLNKF 75 FP+QNLP GVF + S PR VAIG+ + DL A EAGLFDG + LN F Sbjct: 20 FPLQNLPLGVFSL-NGSAPRSGVAIGEHIFDLQAALEAGLFDGAAKAAVEATRGGQLNAF 78 Query: 76 LAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFFAS 135 +GR A R L + + + + K + EM +P I DYTDF+ Sbjct: 79 FELGREARVALRERLLELFAEGSTLHGKIEAQGAKLLPLAADCEMHLPAKINDYTDFYVG 138 Query: 136 MHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEPYF 195 + HA+N G +FR P+N + PN+ +PI YHGRAS+I SGTD+ RP+GQ P G SEP F Sbjct: 139 IEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQSEPTF 197 Query: 196 GPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLGPF 255 GP +LD+ELE+ +G GN++G I + +AADHI G L+NDWSARDIQAWEY PLGPF Sbjct: 198 GPCARLDYELELGIWIGQGNDMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPLGPF 257 Query: 256 LGKSFGTTISPWIVTLDALEPFGCQAPKQ---DPPPLPYLAEKE---SVNYDISLEVQLK 309 L KSF T+ISPW+VT +ALEPF P + DP PLPYL +K + +DI LEV L Sbjct: 258 LSKSFITSISPWVVTAEALEPFRRAQPARPQGDPQPLPYLLDKRDQAAGAFDIELEVLLL 317 Query: 310 PSGRDDSCV----ITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDSYG 365 + + +T SN ++YWT+ Q +AHH+VNGC L+ GDL G+GT+SGP+ +G Sbjct: 318 TEAMREQNLPAHRLTLSNTGHMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPQSGQFG 377 Query: 366 CLLELTWNGQKPLSL-NGTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIVPS 419 LLE+T G+KP+ L +G + FLEDGD++ G C+ DG+ ++GFG C GK++P+ Sbjct: 378 SLLEITEGGKKPIELASGEVRKFLEDGDEIILRGRCRRDGFASIGFGECRGKVLPA 433 Lambda K H 0.319 0.139 0.434 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: 607 Number of extensions: 36 Number of successful extensions: 7 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: 421 Length of database: 434 Length adjustment: 32 Effective length of query: 389 Effective length of database: 402 Effective search space: 156378 Effective search space used: 156378 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate PfGW456L13_4961 (Fumarylacetoacetase (EC 3.7.1.2))
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))
# 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/TIGR01266.hmm # target sequence database: /tmp/gapView.4954.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01266 [M=420] Accession: TIGR01266 Description: fum_ac_acetase: fumarylacetoacetase 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-195 635.1 0.0 2.9e-195 634.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 Fumarylacetoacetase (EC 3.7.1.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 Fumarylacetoacetase (EC 3.7.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 634.9 0.0 2.9e-195 2.9e-195 1 419 [. 9 433 .. 9 434 .] 0.96 Alignments for each domain: == domain 1 score: 634.9 bits; conditional E-value: 2.9e-195 TIGR01266 1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfegl 54 s+va+a+ ++dfplqnlP+Gvfs ++s +r gvaiG++i+dl+++++aglf+g lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 9 SWVASANgHADFPLQNLPLGVFS-LNGSAPRSGVAIGEHIFDLQAALEAGLFDG- 61 8******9***************.8899**************************. PP TIGR01266 55 alkehqevfkestlnaflalgrparkevrerlqkllsesaevlrdnaalrk.eal 108 a+k++ e+++++ lnaf+ lgr ar+++rerl++l++e + +l + + + ++l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 62 AAKAAVEATRGGQLNAFFELGREARVALRERLLELFAEGS-TLHGKIEAQGaKLL 115 99***********************************655.56666666650555 PP TIGR01266 109 laqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallPnykhlPvgyhGr 163 +a+++mhlPa+i dytdfy++i+ha+nvG+lfr +dn+llPnyk++P+gyhGr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 116 PLAADCEMHLPAKINDYTDFYVGIEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGR 169 5678*******************************.******************* PP TIGR01266 164 assvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavp 218 as+++ sGt++rrP+Gq+++++ +eP+fgpc++ld+elel++++g++n++G+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 170 ASTIRPSGTDVRRPKGQTLPAGQSEPTFGPCARLDYELELGIWIGQGNDMGDSIA 224 ******************************************************* PP TIGR01266 219 iekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273 i a++hi+G++llndwsardiqawey+PlGPfl+ksf+t++sPwvv++ealePf lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 225 IGDAADHIAGFCLLNDWSARDIQAWEYQPLGPFLSKSFITSISPWVVTAEALEPF 279 ******************************************************* PP TIGR01266 274 rvaq.lePeqdpkplpylredr..adtafdielevslkteGlae....aavisrs 321 r+aq ++P++dp+plpyl ++r a afdielev l te ++e a++++ s lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 280 RRAQpARPQGDPQPLPYLLDKRdqAAGAFDIELEVLLLTEAMREqnlpAHRLTLS 334 ****9**************999556789***************9899889***** PP TIGR01266 322 nakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkke 376 n+ ++ywt++q++ahhsvnGc+l+aGdl+gsGt+sG++ ++fGslle++ +Gkk+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 335 NTGHMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPQSGQFGSLLEITEGGKKP 389 ******************************************************* PP TIGR01266 377 vkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419 ++la+ge+rkfledGde+ilrg+c+++G +GfGec+Gkvlpa lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4961 390 IELASGEVRKFLEDGDEIILRGRCRRDGFAsIGFGECRGKVLPA 433 ****************************988************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (434 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.63 // [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