Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate Pf6N2E2_5291 Fumarylacetoacetase (EC 3.7.1.2)
Query= SwissProt::P16930 (419 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 Length = 434 Score = 378 bits (971), Expect = e-109 Identities = 207/420 (49%), Positives = 262/420 (62%), Gaps = 18/420 (4%) Query: 10 SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKH--LFTGPVLSKHQDVFNQPTL 67 +DFP+ NLP G+FS G R GVAIG++I DL H LF G + + L Sbjct: 18 ADFPLQNLPLGIFSVDGGAL-RSGVAIGERIFDLQAALHAGLFDGAA-RQAVEAMADGQL 75 Query: 68 NSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQAS-ATMHLPATIGDYTD 126 N F LG+ A R L LL + LR + E + + A+ MHLPA I DYTD Sbjct: 76 NGFFDLGRGARVALRERLLELLR-EDSPLRGEVEAQGAKLLLLAADCQMHLPARINDYTD 134 Query: 127 FYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDSK 186 FY +HA NVG +FR +N L+PN+ ++P+GYHGRAS++ SGT +RRP GQ P Sbjct: 135 FYVGIEHAQNVGKLFRP-DNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQT 193 Query: 187 PPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYVP 246 P +G C LD ELE+ ++G GN LGEPIPI A EHI G L+NDWSARDIQ WEY P Sbjct: 194 EPTFGPCARLDYELELGIWIGKGNALGEPIPIGDAAEHIGGFCLLNDWSARDIQAWEYQP 253 Query: 247 LGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQ---DPRPLPYLCHDEPY---TFDINLS 300 LGPFL KSF T++SPWVV +AL PF P P + DP+PLPYL FDI L Sbjct: 254 LGPFLSKSFLTSISPWVVTAEALEPFRRPQPARPQGDPQPLPYLLDKRDQAGGAFDIELE 313 Query: 301 VNLKGEGMSQ----AATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEP 356 V L E M + A + SN +YMYWT+ Q + HHSVNGC L+ GDL SGT+SGPE Sbjct: 314 VLLLTEAMGEQNLPAQRLTLSNTQYMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPEN 373 Query: 357 ENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGY-RIGFGQCAGKVLPA 415 FGS+LE++ G KPI+L +G+ R+FL DGDE+I+ C+ +G+ IGFG+C GK+LPA Sbjct: 374 HQFGSLLEITEGGKKPIELASGEVRRFLEDGDEIILRARCRREGFASIGFGECRGKILPA 433 Lambda K H 0.321 0.139 0.440 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: 616 Number of extensions: 41 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: 419 Length of database: 434 Length adjustment: 32 Effective length of query: 387 Effective length of database: 402 Effective search space: 155574 Effective search space used: 155574 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: 51 (24.3 bits)
Align candidate Pf6N2E2_5291 (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.5748.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-193 629.5 0.0 1.4e-193 629.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 Fumarylacetoacetase (EC 3.7.1.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 Fumarylacetoacetase (EC 3.7.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.4 0.0 1.4e-193 1.4e-193 1 419 [. 9 433 .. 9 434 .] 0.96 Alignments for each domain: == domain 1 score: 629.4 bits; conditional E-value: 1.4e-193 TIGR01266 1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevf 63 s+va a+ ++dfplqnlP+G+fs + r gvaiG++i+dl+++++aglf+g a++++ e++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 9 SWVACANgHADFPLQNLPLGIFS-VDGGALRSGVAIGERIFDLQAALHAGLFDG-AARQAVEAM 70 8******9***************.56677889**********************.89999**** PP TIGR01266 64 kestlnaflalgrparkevrerlqkllsesaevlrdnaalr.keallaqaeatmhlPaqiGdyt 126 ++ ln f+ lgr ar+++rerl++ll e++ lr + + + ++ll +a+++mhlPa+i dyt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 71 ADGQLNGFFDLGRGARVALRERLLELLREDSP-LRGEVEAQgAKLLLLAADCQMHLPARINDYT 133 ****************************7765.5777665527899999*************** PP TIGR01266 127 dfyssirhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePv 190 dfy++i+ha+nvG+lfr +dn+llPnyk++P+gyhGras+++ sGt++rrP+Gq+++++ eP+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 134 DFYVGIEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQTEPT 196 *****************.********************************************** PP TIGR01266 191 fgpckkldlelelaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflak 254 fgpc++ld+elel++++g++n+lGe++pi a+ehi G++llndwsardiqawey+PlGPfl+k lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 197 FGPCARLDYELELGIWIGKGNALGEPIPIGDAAEHIGGFCLLNDWSARDIQAWEYQPLGPFLSK 260 **************************************************************** PP TIGR01266 255 sfattvsPwvvsiealePfrvaq.lePeqdpkplpylredr..adtafdielevslkteGlae. 314 sf t++sPwvv++ealePfr++q ++P++dp+plpyl ++r a afdielev l te ++e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 261 SFLTSISPWVVTAEALEPFRRPQpARPQGDPQPLPYLLDKRdqAGGAFDIELEVLLLTEAMGEq 324 ***********************9***************99546689*************9998 PP TIGR01266 315 ...aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkk 375 a++++ sn++ +ywt++q++ahhsvnGc+l+aGdl+gsGt+sG+e+++fGslle++ +Gkk lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 325 nlpAQRLTLSNTQYMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPENHQFGSLLEITEGGKK 388 89889*********************************************************** PP TIGR01266 376 evkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419 +++la+ge+r+fledGde+ilr++c++eG +GfGec+Gk+lpa lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5291 389 PIELASGEVRRFLEDGDEIILRARCRREGFAsIGFGECRGKILPA 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: 00:00:00.01 # Mc/sec: 10.70 // [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