Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_013289899.1 CALHY_RS10305 class II fructose-1,6-bisphosphate aldolase
Query= BRENDA::O97447 (323 letters) >NCBI__GCF_000166355.1:WP_013289899.1 Length = 323 Score = 310 bits (793), Expect = 4e-89 Identities = 174/325 (53%), Positives = 221/325 (68%), Gaps = 12/325 (3%) Query: 1 MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60 MPL T R+M +A + KY +GAFNVNNME IQGI++A + ++P+ILQ S GA KY+ I Sbjct: 1 MPLVTTREMFKKAAEGKYAIGAFNVNNMEIIQGIVEAAKEEQAPLILQVSAGARKYAKHI 60 Query: 61 YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120 YL KL EAALE D+PI +HLDHG+ E K ID GF+SVMID S PF+EN+ +TK+ Sbjct: 61 YLIKLVEAALEDSGDLPIALHLDHGEDFEICKACIDGGFTSVMIDGSRLPFEENIALTKK 120 Query: 121 VVAYAHARSVSVEAELGTLGGIEEDV---QNTVQLTEPQDAKKFVELTGVDALAVAIGTS 177 VV YAH R V VEAELG L GIE++V ++ T+P A +FVE TGVD+LAVAIGTS Sbjct: 121 VVEYAHERGVVVEAELGKLAGIEDNVKVAEHEAAFTDPDQAAEFVERTGVDSLAVAIGTS 180 Query: 178 HGAYKFKSESDIRLAIDRVKTISDL--TGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVG 235 HGAYKFK D RL +R++ I + P+V+HG+S+V + +M NKYGG +P A G Sbjct: 181 HGAYKFK--GDPRLDFERLQKIVEKLPKDFPIVLHGASTVLPEFVEMCNKYGGNIPGAKG 238 Query: 236 VPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLI 295 VP + + A GV KIN+D+D R+AMT AIRK EHP+ FDPR YL GRDAI EM+ Sbjct: 239 VPEDMLRKAAELGVRKINIDTDLRLAMTAAIRKHLYEHPDHFDPRQYLKDGRDAIKEMVK 298 Query: 296 PKIK-AFGSAGHAGDYKVVSLEEAK 319 K++ G AG A + LEE K Sbjct: 299 HKLRNVLGCAGKAPEI----LEEIK 319 Lambda K H 0.318 0.135 0.389 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: 331 Number of extensions: 8 Number of successful extensions: 3 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: 323 Length adjustment: 28 Effective length of query: 295 Effective length of database: 295 Effective search space: 87025 Effective search space used: 87025 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 WP_013289899.1 CALHY_RS10305 (class II fructose-1,6-bisphosphate aldolase)
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.3589792.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-118 381.5 0.2 1.8e-118 381.3 0.2 1.1 1 NCBI__GCF_000166355.1:WP_013289899.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166355.1:WP_013289899.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.3 0.2 1.8e-118 1.8e-118 1 282 [] 3 311 .. 3 311 .. 0.98 Alignments for each domain: == domain 1 score: 381.3 bits; conditional E-value: 1.8e-118 TIGR01859 1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 lv+++e+++ka ++kYa+gafn+nn+e++q i+eaa+ee++P+i+qvs ga+kY+ +++lv+a++e+ NCBI__GCF_000166355.1:WP_013289899.1 3 LVTTREMFKKAAEGKYAIGAFNVNNMEIIQGIVEAAKEEQAPLILQVSAGARKYAK-HIYLIKLVEAALEDSG 74 79*****************************************************9.667889********** PP TIGR01859 74 ivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGiedd.. 144 ++P+alhLDhG+++e c ++i+ Gf+svmiD+s+lp+een+++tkkvve+ah++gv veaelGkl+Gied+ NCBI__GCF_000166355.1:WP_013289899.1 75 DLPIALHLDHGEDFEICKACIDGGFTSVMIDGSRLPFEENIALTKKVVEYAHERGVVVEAELGKLAGIEDNvk 147 ***********************************************************************88 PP TIGR01859 145 vvekeaeladideakklvketgvDaLaiaiGtshG..kykgepkldferlkeikklln..lPlvlhGas.... 209 v e+ea ++d+d+a ++v++tgvD+La+aiGtshG k+kg+p+ldferl++i ++l+ +P+vlhGas NCBI__GCF_000166355.1:WP_013289899.1 148 VAEHEAAFTDPDQAAEFVERTGVDSLAVAIGTSHGayKFKGDPRLDFERLQKIVEKLPkdFPIVLHGAStvlp 220 8899*******************************9999999************999878************* PP TIGR01859 210 .................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilapareal 265 G+pe++l+ka++lg+ k+nidtdlrla+taairk+l e+ d++dpR++l+++r+a+ NCBI__GCF_000166355.1:WP_013289899.1 221 efvemcnkyggnipgakGVPEDMLRKAAELGVRKINIDTDLRLAMTAAIRKHLYEHPDHFDPRQYLKDGRDAI 293 ************************************************************************* PP TIGR01859 266 kevvkekik.vlgsagka 282 ke+vk+k++ vlg agka NCBI__GCF_000166355.1:WP_013289899.1 294 KEMVKHKLRnVLGCAGKA 311 ********9899*99997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (282 nodes) Target sequences: 1 (323 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.14 // [ok]
This GapMind analysis is from Sep 24 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