Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_003473390.1 J416_RS13030 class II fructose-1,6-bisphosphate aldolase
Query= SwissProt::P13243 (285 letters) >NCBI__GCF_000359605.1:WP_003473390.1 Length = 285 Score = 456 bits (1172), Expect = e-133 Identities = 227/285 (79%), Positives = 250/285 (87%), Gaps = 1/285 (0%) Query: 1 MPLVSMTEMLNTAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGF 60 MPLVSM EML A + Y VGQFNLNNLE+ QAILQAAEEE+SPVILGVSEGAG+YMGGF Sbjct: 1 MPLVSMKEMLEDANKNRYGVGQFNLNNLEYAQAILQAAEEEQSPVILGVSEGAGKYMGGF 60 Query: 61 KTVVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATT 120 K VV+MVKALMEEY TVPVAIHLDHGSSFE+CAKAIHAGFTSVMIDASH PFEENVA T Sbjct: 61 KVVVSMVKALMEEYGTTVPVAIHLDHGSSFEACAKAIHAGFTSVMIDASHDPFEENVALT 120 Query: 121 AKVVELAHFHGVSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSV 180 +KVVELAHFHGVSVEAELGTVGG ED V G+IYAD EC+ELVERTG+DCLAPALGSV Sbjct: 121 SKVVELAHFHGVSVEAELGTVGGTEDGVTG-GIIYADANECKELVERTGVDCLAPALGSV 179 Query: 181 HGPYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQISS 240 HGPY+GEPNLGFKEMEEI G+PLVLHGGTGIP+ DIKK++S GT+KINVNTENQ++ Sbjct: 180 HGPYQGEPNLGFKEMEEINTVAGVPLVLHGGTGIPSEDIKKALSFGTSKINVNTENQMAQ 239 Query: 241 AKAVRETLAAKPDEYDPRKYLGPAREAIKETVIGKMREFGSSNQA 285 +AVR+ L KP+ YDPRKYLGP R+AIKE VIGKMREF SSN+A Sbjct: 240 TEAVRKVLKEKPELYDPRKYLGPGRDAIKEIVIGKMREFSSSNKA 284 Lambda K H 0.313 0.131 0.367 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: 395 Number of extensions: 10 Number of successful extensions: 2 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: 285 Length of database: 285 Length adjustment: 26 Effective length of query: 259 Effective length of database: 259 Effective search space: 67081 Effective search space used: 67081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_003473390.1 J416_RS13030 (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.1255922.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-132 427.0 0.7 2.4e-132 426.8 0.7 1.0 1 NCBI__GCF_000359605.1:WP_003473390.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359605.1:WP_003473390.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 426.8 0.7 2.4e-132 2.4e-132 1 282 [] 3 284 .. 3 284 .. 0.99 Alignments for each domain: == domain 1 score: 426.8 bits; conditional E-value: 2.4e-132 TIGR01859 1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 lv++ke+le+a+k++Y+vg+fn+nnle++qail+aaeee+sPvi+ vsega kY+gg+kvvv++vkal+e++ NCBI__GCF_000359605.1:WP_003473390.1 3 LVSMKEMLEDANKNRYGVGQFNLNNLEYAQAILQAAEEEQSPVILGVSEGAGKYMGGFKVVVSMVKALMEEYG 75 79**********************************************************************9 PP TIGR01859 74 i.vPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddv 145 + vPva+hLDhGss+e+c+kai+aGf+svmiDash p+een+++t+kvve+ah +gvsveaelG++gG+ed+v NCBI__GCF_000359605.1:WP_003473390.1 76 TtVPVAIHLDHGSSFEACAKAIHAGFTSVMIDASHDPFEENVALTSKVVELAHFHGVSVEAELGTVGGTEDGV 148 99*********************************************************************** PP TIGR01859 146 vekeaeladideakklvketgvDaLaiaiGtshGkykgepkldferlkeikkllnlPlvlhGasGipeeqlkk 218 ++ +ad +e+k+lv++tgvD+La+a+G++hG+y+gep+l f++++ei+ + +PlvlhG++Gip+e++kk NCBI__GCF_000359605.1:WP_003473390.1 149 TG-GIIYADANECKELVERTGVDCLAPALGSVHGPYQGEPNLGFKEMEEINTVAGVPLVLHGGTGIPSEDIKK 220 **.9********************************************************************* PP TIGR01859 219 aiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekikvlgsagka 282 a++ g++k+n++t++++a t+a+rkvl+ek + ydpRk+l+p+r+a+ke+v+ k++++ s++ka NCBI__GCF_000359605.1:WP_003473390.1 221 ALSFGTSKINVNTENQMAQTEAVRKVLKEKPELYDPRKYLGPGRDAIKEIVIGKMREFSSSNKA 284 **************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (282 nodes) Target sequences: 1 (285 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.75 // [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