Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate RR42_RS03215 RR42_RS03215 fructose-bisphosphate aldolase
Query= SwissProt::Q56815 (354 letters) >FitnessBrowser__Cup4G11:RR42_RS03215 Length = 354 Score = 531 bits (1367), Expect = e-155 Identities = 265/353 (75%), Positives = 302/353 (85%) Query: 1 MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60 M LVSMRQLLDHAA++ Y LPAFNVNN+EQV+AIM AA ++PVI+Q SAGARKYAGE Sbjct: 1 MPLVSMRQLLDHAAENGYALPAFNVNNLEQVQAIMQAADEVNAPVIMQASAGARKYAGEH 60 Query: 61 FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120 FLRHLI AAVEAYP IPVVMHQDHG SPA+C AI GFSSVMMDGSL+EDGKTP+DY+Y Sbjct: 61 FLRHLIEAAVEAYPHIPVVMHQDHGQSPAICQAAIDLGFSSVMMDGSLREDGKTPSDYEY 120 Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180 N+ VT KVV+L+HA+GV+VEGELGCLGSLETG+ EDG GAE LDHS LLTDP++AA Sbjct: 121 NIEVTRKVVQLSHAIGVTVEGELGCLGSLETGEAGEEDGIGAEGKLDHSMLLTDPEQAAD 180 Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240 FVKATQ DALAIAIGTSHGAYKFTRKPTGDILAI+RIK IH RIP THLVMHGSSSVPQE Sbjct: 181 FVKATQLDALAIAIGTSHGAYKFTRKPTGDILAINRIKEIHARIPNTHLVMHGSSSVPQE 240 Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300 LL EIR +GGD+KETYGVPVEEIQ+ I+YGVRK+NIDTDIRLAMT AIRR A+N S+FD Sbjct: 241 LLAEIRQFGGDMKETYGVPVEEIQDAIKYGVRKINIDTDIRLAMTGAIRRFFAENPSKFD 300 Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353 PR+++ A E AK VC AR+ AFG G+A KI+ + LD +A++Y SGELAQVV Sbjct: 301 PREYLKPAREAAKLVCKARYVAFGCEGQAAKIKPVSLDAIAQKYKSGELAQVV 353 Lambda K H 0.316 0.132 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: 459 Number of extensions: 12 Number of successful extensions: 1 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: 354 Length of database: 354 Length adjustment: 29 Effective length of query: 325 Effective length of database: 325 Effective search space: 105625 Effective search space used: 105625 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: 49 (23.5 bits)
Align candidate RR42_RS03215 RR42_RS03215 (fructose-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (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/TIGR01521.hmm # target sequence database: /tmp/gapView.4644.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01521 [M=347] Accession: TIGR01521 Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype 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-191 621.9 0.4 1.7e-191 621.7 0.4 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS03215 RR42_RS03215 fructose-bisphospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS03215 RR42_RS03215 fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 621.7 0.4 1.7e-191 1.7e-191 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 621.7 bits; conditional E-value: 1.7e-191 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 l+s+rqlldhaae+gy +pafnvnnleq+ aim+aad+ ++pvi+qas+gar+yage +lr+l++aave lcl|FitnessBrowser__Cup4G11:RR42_RS03215 3 LVSMRQLLDHAAENGYALPAFNVNNLEQVQAIMQAADEVNAPVIMQASAGARKYAGEHFLRHLIEAAVE 71 69******************************************************************* PP TIGR01521 70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138 yp+ipvv+hqdhg+spa+c++ai lgf+svmmdgsl+ed+ktp+dy+yn++vt +vv+l+ha+g++ve lcl|FitnessBrowser__Cup4G11:RR42_RS03215 72 AYPHIPVVMHQDHGQSPAICQAAIDLGFSSVMMDGSLREDGKTPSDYEYNIEVTRKVVQLSHAIGVTVE 140 ********************************************************************* PP TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207 gelgclgsletg++++edg g+eg+ld+s lltdpe+aa+fvk t++dala+aigtshgaykftrkptg lcl|FitnessBrowser__Cup4G11:RR42_RS03215 141 GELGCLGSLETGEAGEEDGIGAEGKLDHSMLLTDPEQAADFVKATQLDALAIAIGTSHGAYKFTRKPTG 209 ********************************************************************* PP TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276 ++lai+ri+eih+r+p+thlvmhgsssvpqe l+ i ++gg++ketygvpveei+ ik+gvrk+nidt lcl|FitnessBrowser__Cup4G11:RR42_RS03215 210 DILAINRIKEIHARIPNTHLVMHGSSSVPQELLAEIRQFGGDMKETYGVPVEEIQDAIKYGVRKINIDT 278 ********************************************************************* PP TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345 d rla+t+a+rr+ a++ps+fdpr++lk+a ea k vckary afg g+a+kik+vsl+ +a++y +g lcl|FitnessBrowser__Cup4G11:RR42_RS03215 279 DIRLAMTGAIRRFFAENPSKFDPREYLKPAREAAKLVCKARYVAFGCEGQAAKIKPVSLDAIAQKYKSG 347 ********************************************************************* PP TIGR01521 346 el 347 el lcl|FitnessBrowser__Cup4G11:RR42_RS03215 348 EL 349 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (354 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: 8.33 // [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