Align Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate 8499233 DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq)
Query= SwissProt::A8B2U2 (323 letters) >FitnessBrowser__Miya:8499233 Length = 307 Score = 294 bits (752), Expect = 2e-84 Identities = 159/301 (52%), Positives = 205/301 (68%), Gaps = 5/301 (1%) Query: 1 MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60 MPL +QM A K Y +GAFNVNNME IQGIM+A + ++P+ILQ S GA KY+ Sbjct: 1 MPLTGPKQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAGQN 60 Query: 61 YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120 Y+ KL EAAL D+P+ +HLDHG K ID GF+SVM D SH P++EN+ +T++ Sbjct: 61 YIVKLIEAAL-MDTDLPVVLHLDHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVTRQ 119 Query: 121 VVAYAHARGVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAIGTSHG 179 VV YAHARGV VEAELG L G+E++V + T+P A FV+ TG D+LA+AIGTSHG Sbjct: 120 VVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVDFVKRTGCDSLAIAIGTSHG 179 Query: 180 AYKFKSESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPI 238 AYKF E+ + A R++ I+ L G PLV+HG+SSVP++ DM N YGGK+ A GVP Sbjct: 180 AYKFTGEAKLDFA--RLEKITSMLPGYPLVLHGASSVPQEFVDMANTYGGKVGSAKGVPE 237 Query: 239 ESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKI 298 + + A GVCKIN+D+D R+AMT IRK F+E P FDPR YL P RDA+ M+ KI Sbjct: 238 DLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKI 297 Query: 299 K 299 + Sbjct: 298 R 298 Lambda K H 0.318 0.135 0.391 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: 289 Number of extensions: 10 Number of successful extensions: 4 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: 323 Length of database: 307 Length adjustment: 27 Effective length of query: 296 Effective length of database: 280 Effective search space: 82880 Effective search space used: 82880 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: 48 (23.1 bits)
Align candidate 8499233 DvMF_0013 (fructose-1,6-bisphosphate aldolase, class II (RefSeq))
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (EC 4.1.2.13))
# 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.aa/TIGR01859.hmm # target sequence database: /tmp/gapView.27739.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01859 [M=282] Accession: TIGR01859 Description: fruc_bis_ald_: fructose-1,6-bisphosphate aldolase, class II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-117 376.4 0.0 8.7e-117 375.8 0.0 1.3 1 lcl|FitnessBrowser__Miya:8499233 DvMF_0013 fructose-1,6-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499233 DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.8 0.0 8.7e-117 8.7e-117 5 282 .] 7 307 .] 3 307 .] 0.98 Alignments for each domain: == domain 1 score: 375.8 bits; conditional E-value: 8.7e-117 TIGR01859 5 kellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkalieklsivPvalhL 81 k+++e+a+ke+Ya+gafn+nn+e++q i++aa ee++P+i+qvs ga+kY+g + +v+l++a++ ++ +Pv+lhL lcl|FitnessBrowser__Miya:8499233 7 KQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAG-QNYIVKLIEAALMDTD-LPVVLHL 81 89*************************************************9.999******9999888.9****** PP TIGR01859 82 DhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvvekeaeladidea 158 DhG++++ c ++i+ Gf+svm+D+shlp+een++ t++vve+aha+gv veaelG+l+G+ed+v +++++++d+d+a lcl|FitnessBrowser__Miya:8499233 82 DHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVTRQVVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQA 158 ***************************************************************************** PP TIGR01859 159 kklvketgvDaLaiaiGtshG..kykgepkldferlkeikklln.lPlvlhGas.....................Gi 211 ++vk+tg D+LaiaiGtshG k++ge+kldf+rl++i+ +l+ PlvlhGas G+ lcl|FitnessBrowser__Miya:8499233 159 VDFVKRTGCDSLAIAIGTSHGayKFTGEAKLDFARLEKITSMLPgYPLVLHGASsvpqefvdmantyggkvgsakGV 235 *********************999999*****************9******************************** PP TIGR01859 212 peeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekik.vlgsagka 282 pe+ l+ka+++g++k+nidtd+rla+ta+irk++ ek +dpR +l+par+a+k++v++ki+ vlg ++k+ lcl|FitnessBrowser__Miya:8499233 236 PEDLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKIRnVLGCSNKI 307 **************************************************************9899*99996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (282 nodes) Target sequences: 1 (307 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: 3.10 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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