Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011648981.1 RLEG_RS26325 fructose-bisphosphate aldolase class II
Query= BRENDA::A0Q7I9 (354 letters) >NCBI__GCF_000023185.1:WP_011648981.1 Length = 354 Score = 461 bits (1186), Expect = e-134 Identities = 226/351 (64%), Positives = 274/351 (78%) Query: 1 MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60 MA ++LRQLLDHAAE GYG+PAFN+NN+EQ A+MEAAD ++PVI+Q S GAR YA Sbjct: 1 MARITLRQLLDHAAEEGYGVPAFNINNMEQALAIMEAADACHAPVIMQASRGARAYAHDI 60 Query: 61 FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120 ++H++ A +E YPHIPVC+H DHG PS C +IQ GF+SVMMDGSLK+D KTPAD+ Y Sbjct: 61 MLKHMMDAVVEIYPHIPVCVHLDHGNDPSNCMTAIQAGFTSVMMDGSLKADAKTPADWAY 120 Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180 NV VTK V+DMAH G+SVEGELG LGSLETG EDG GAEG LS DQLLTDP+EA Sbjct: 121 NVGVTKMVTDMAHFGGISVEGELGVLGSLETGMGEAEDGHGAEGKLSHDQLLTDPDEAVK 180 Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240 FVR TKVDALAIA+GTSHGAYKFT+ P G VL++ ++EIH ++P+THLVMHGSSSVP + Sbjct: 181 FVRETKVDALAIAMGTSHGAYKFTRKPDGSVLAMNVIEEIHRKLPNTHLVMHGSSSVPIE 240 Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300 E+IN YGG M T+GVPVEEI IK GVRK+NIDTD RMA TG IRR L E+P+EFD Sbjct: 241 LQEIINKYGGQMKPTWGVPVEEIQRGIKNGVRKVNIDTDGRMAMTGQIRRVLQEDPSEFD 300 Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELDP 351 PRKY A A++++C R+E FG+AGMA +I P+ + M +RY+SG LDP Sbjct: 301 PRKYLKPAMTALTKLCKERFEQFGTAGMAGRITPLPVSEMAKRYKSGSLDP 351 Lambda K H 0.316 0.132 0.380 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: 483 Number of extensions: 11 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 WP_011648981.1 RLEG_RS26325 (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.11115.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-187 608.7 0.4 1.7e-187 608.5 0.4 1.0 1 lcl|NCBI__GCF_000023185.1:WP_011648981.1 RLEG_RS26325 fructose-bisphospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_011648981.1 RLEG_RS26325 fructose-bisphosphate aldolase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 608.5 0.4 1.7e-187 1.7e-187 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 608.5 bits; conditional E-value: 1.7e-187 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 +i+lrqlldhaae+gygvpafn+nn+eq laimeaad++ +pvi+qasrgar ya + +l++++ a+ve lcl|NCBI__GCF_000023185.1:WP_011648981.1 3 RITLRQLLDHAAEEGYGVPAFNINNMEQALAIMEAADACHAPVIMQASRGARAYAHDIMLKHMMDAVVE 71 69******************************************************************* PP TIGR01521 70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138 yp+ipv++h dhgn+p+ c++aiq gftsvmmdgslk+daktpad+ ynv vt+ v+ +ah g+sve lcl|NCBI__GCF_000023185.1:WP_011648981.1 72 IYPHIPVCVHLDHGNDPSNCMTAIQAGFTSVMMDGSLKADAKTPADWAYNVGVTKMVTDMAHFGGISVE 140 ********************************************************************* PP TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207 gelg lgsletg+geaedghg+eg+l + qlltdp+ea++fv++tkvdala+a+gtshgaykftrkp g lcl|NCBI__GCF_000023185.1:WP_011648981.1 141 GELGVLGSLETGMGEAEDGHGAEGKLSHDQLLTDPDEAVKFVRETKVDALAIAMGTSHGAYKFTRKPDG 209 ********************************************************************* PP TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276 vla+++ieeih++lp+thlvmhgsssvp e +++in+ygg++k t+gvpveei++gik gvrkvnidt lcl|NCBI__GCF_000023185.1:WP_011648981.1 210 SVLAMNVIEEIHRKLPNTHLVMHGSSSVPIELQEIINKYGGQMKPTWGVPVEEIQRGIKNGVRKVNIDT 278 ********************************************************************* PP TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345 d r+a+t+ +rrv+++dpsefdprk+lk+a+ a+ ++ck+r+e+fgtag a +i ++++ ema+ry +g lcl|NCBI__GCF_000023185.1:WP_011648981.1 279 DGRMAMTGQIRRVLQEDPSEFDPRKYLKPAMTALTKLCKERFEQFGTAGMAGRITPLPVSEMAKRYKSG 347 ********************************************************************* PP TIGR01521 346 el 347 +l lcl|NCBI__GCF_000023185.1:WP_011648981.1 348 SL 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: 7.39 // [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