Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_028989695.1 G579_RS0107525 fructose-bisphosphate aldolase class II
Query= SwissProt::Q56815 (354 letters) >NCBI__GCF_000423825.1:WP_028989695.1 Length = 365 Score = 531 bits (1367), Expect = e-155 Identities = 258/349 (73%), Positives = 302/349 (86%) Query: 1 MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60 MAL+SMRQLLDHAA+ YG+PAFNVNNMEQ+ AIM+AA+ +PVILQGSAGARKYAGEP Sbjct: 1 MALISMRQLLDHAAEHGYGIPAFNVNNMEQIHAIMEAAKEVDAPVILQGSAGARKYAGEP 60 Query: 61 FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120 FLRHL+ AAVE YP+IPV MHQDHGASPAVC+ AI+SGF+SVMMDGSL ED KTP+ YDY Sbjct: 61 FLRHLVMAAVEMYPDIPVAMHQDHGASPAVCIQAIRSGFTSVMMDGSLMEDAKTPSTYDY 120 Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180 NV+VT+KVVE+AHAVGVSVEGELGCLGSLE+G GE EDGHGAE L H +LLTDP+EAA+ Sbjct: 121 NVAVTSKVVEMAHAVGVSVEGELGCLGSLESGMGEKEDGHGAEGVLSHDQLLTDPEEAAR 180 Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240 FV AT+ DALAIAIGTSHGAYKF+RKPTGDILAI+R+K IH RIP THLVMHGSSSVPQE Sbjct: 181 FVAATKVDALAIAIGTSHGAYKFSRKPTGDILAIERVKEIHARIPDTHLVMHGSSSVPQE 240 Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300 L+ I +GG++ +TYGVPVEEIQ+GI++GVRKVNIDTD+R+AMT AIR+ A+NKS FD Sbjct: 241 WLDVINEFGGEMPQTYGVPVEEIQQGIKFGVRKVNIDTDLRMAMTGAIRKHLAQNKSNFD 300 Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGEL 349 PRKF+ A + AK +C AR+E FG+AG A KI+ I +D+MA RY GEL Sbjct: 301 PRKFLTEATKAAKAICKARYEQFGTAGNASKIKVIAMDDMAARYKKGEL 349 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: 485 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: 365 Length adjustment: 29 Effective length of query: 325 Effective length of database: 336 Effective search space: 109200 Effective search space used: 109200 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 WP_028989695.1 G579_RS0107525 (fructose-bisphosphate aldolase class II)
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.19826.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-204 664.1 2.6 2.5e-204 663.9 2.6 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028989695.1 G579_RS0107525 fructose-bisphosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028989695.1 G579_RS0107525 fructose-bisphosphate aldolase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 663.9 2.6 2.5e-204 2.5e-204 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 663.9 bits; conditional E-value: 2.5e-204 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 lis+rqlldhaae+gyg+pafnvnn+eqi aimeaa++ d+pvilq s+gar+yage++lr+lv+aave lcl|NCBI__GCF_000423825.1:WP_028989695.1 3 LISMRQLLDHAAEHGYGIPAFNVNNMEQIHAIMEAAKEVDAPVILQGSAGARKYAGEPFLRHLVMAAVE 71 69******************************************************************* PP TIGR01521 70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138 +ypdipv++hqdhg+spa+c +ai+ gftsvmmdgsl edaktp+ ydynv vt++vv++ahavg+sve lcl|NCBI__GCF_000423825.1:WP_028989695.1 72 MYPDIPVAMHQDHGASPAVCIQAIRSGFTSVMMDGSLMEDAKTPSTYDYNVAVTSKVVEMAHAVGVSVE 140 ********************************************************************* PP TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207 gelgclgsle+g+ge+edghg+eg+l + qlltdpeeaa+fv+ tkvdala+aigtshgaykf+rkptg lcl|NCBI__GCF_000423825.1:WP_028989695.1 141 GELGCLGSLESGMGEKEDGHGAEGVLSHDQLLTDPEEAARFVAATKVDALAIAIGTSHGAYKFSRKPTG 209 ********************************************************************* PP TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276 ++lai+r++eih+r+pdthlvmhgsssvpqewldvine+gge+++tygvpveei++gikfgvrkvnidt lcl|NCBI__GCF_000423825.1:WP_028989695.1 210 DILAIERVKEIHARIPDTHLVMHGSSSVPQEWLDVINEFGGEMPQTYGVPVEEIQQGIKFGVRKVNIDT 278 ********************************************************************* PP TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345 dlr+a+t+a+r+ +a+++s+fdprkfl +a +a k++ckarye+fgtagnaskikv+++++ma+ry kg lcl|NCBI__GCF_000423825.1:WP_028989695.1 279 DLRMAMTGAIRKHLAQNKSNFDPRKFLTEATKAAKAICKARYEQFGTAGNASKIKVIAMDDMAARYKKG 347 ********************************************************************* PP TIGR01521 346 el 347 el lcl|NCBI__GCF_000423825.1:WP_028989695.1 348 EL 349 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (365 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: 8.64 // [ok]
This GapMind analysis is from Apr 10 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