Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 207620 DVU2143 fructose-1,6-bisphosphate aldolase, class II
Query= BRENDA::Q9RHA2 (305 letters) >MicrobesOnline__882:207620 Length = 307 Score = 285 bits (729), Expect = 9e-82 Identities = 148/292 (50%), Positives = 204/292 (69%), Gaps = 4/292 (1%) Query: 7 EILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRALTLMAVE 66 E+ +A EG+ VGAFNVNNME +Q +++A E+R+P+IL +S GA KY G+ + +E Sbjct: 8 EMFARAYREGHAVGAFNVNNMEIIQGIMQAGAEERAPLILQVSAGARKYAGQNYIIKLIE 67 Query: 67 LAK-EARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVEAAHAV 125 A + +PV +HLDHG ++ + GFTSVMID SH +E N+ TRRVVE AH Sbjct: 68 AALLDTDLPVVLHLDHGQDFDICKSCIDGGFTSVMIDGSHLSYEENIAVTRRVVEYAHDK 127 Query: 126 GVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKG 185 GV VEAELG+LAG+E+ V+ + ++ T+P++A F++RTG D LA+AIGTSHGAYK G Sbjct: 128 GVWVEAELGQLAGVEDEVSAEH--SVYTDPDQAVEFVQRTGCDSLAIAIGTSHGAYKFTG 185 Query: 186 RPFIDHARLERIARLVPA-PLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIKKAIS 244 +D ARLE I +++P PLVLHGAS+VP E VE A GG++G A G+ + ++KA + Sbjct: 186 DAKLDFARLETITKMLPDYPLVLHGASSVPQEFVEMANAYGGKVGGARGVPEDLLRKAAT 245 Query: 245 LGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRM 296 G+ KIN DTD+RLA TA IR+ +NP +FDPR YL PAREAVK +V+ ++ Sbjct: 246 FGVCKINIDTDIRLAMTATIRKHFIENPGDFDPRAYLKPAREAVKNMVQHKI 297 Lambda K H 0.317 0.134 0.369 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: 257 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: 305 Length of database: 307 Length adjustment: 27 Effective length of query: 278 Effective length of database: 280 Effective search space: 77840 Effective search space used: 77840 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate 207620 DVU2143 (fructose-1,6-bisphosphate aldolase, class II)
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.carbon/TIGR01859.hmm # target sequence database: /tmp/gapView.30267.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-113 364.3 0.1 8.5e-113 362.7 0.1 1.6 1 lcl|MicrobesOnline__882:207620 DVU2143 fructose-1,6-bisphosphat Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207620 DVU2143 fructose-1,6-bisphosphate aldolase, class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.7 0.1 8.5e-113 8.5e-113 5 282 .] 7 307 .] 3 307 .] 0.98 Alignments for each domain: == domain 1 score: 362.7 bits; conditional E-value: 8.5e-113 TIGR01859 5 kellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkalieklsivPvalhLDh 83 +e++++a++e++avgafn+nn+e++q i++a+ ee++P+i+qvs ga+kY+g + +++l++a++ ++ +Pv+lhLDh lcl|MicrobesOnline__882:207620 7 REMFARAYREGHAVGAFNVNNMEIIQGIMQAGAEERAPLILQVSAGARKYAG-QNYIIKLIEAALLDTD-LPVVLHLDH 83 69*************************************************9.999*****99998888.********* PP TIGR01859 84 GssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvvekeaeladideakklv 162 G++++ c ++i+ Gf+svmiD+shl++een++ t++vve+ah kgv veaelG+l+G+ed+v +++++++d+d+a ++v lcl|MicrobesOnline__882:207620 84 GQDFDICKSCIDGGFTSVMIDGSHLSYEENIAVTRRVVEYAHDKGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVEFV 162 ******************************************************************************* PP TIGR01859 163 ketgvDaLaiaiGtshG..kykgepkldferlkeikklln.lPlvlhGas.....................Gipeeqlk 217 ++tg D+LaiaiGtshG k++g++kldf+rl++i+k+l+ PlvlhGas G+pe+ l+ lcl|MicrobesOnline__882:207620 163 QRTGCDSLAIAIGTSHGayKFTGDAKLDFARLETITKMLPdYPLVLHGASsvpqefvemanayggkvggarGVPEDLLR 241 *****************8888999***************99************************************** PP TIGR01859 218 kaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekik.vlgsagka 282 ka++ g++k+nidtd+rla+ta+irk++ e+ +dpR +l+parea+k++v++ki+ vlg ++k+ lcl|MicrobesOnline__882:207620 242 KAATFGVCKINIDTDIRLAMTATIRKHFIENPGDFDPRAYLKPAREAVKNMVQHKIRnVLGCSNKI 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 1.81 // [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