Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate YP_001312666.1 Smed_3923 fructose-1,6-bisphosphate aldolase
Query= SwissProt::Q56815 (354 letters) >NCBI__GCF_000017145.1:YP_001312666.1 Length = 359 Score = 464 bits (1194), Expect = e-135 Identities = 229/349 (65%), Positives = 277/349 (79%) Query: 1 MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60 MA +++RQLLDHAA+ SYG+PAFN+NNMEQ AIM+AARA +PVILQ S GAR YA + Sbjct: 1 MARITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARACDAPVILQVSRGARSYANDI 60 Query: 61 FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120 L ++ A YP+IP+ +HQDHG + A C+ AI+ GF+SVMMDGSLKED KTPADY Y Sbjct: 61 MLAKMMEALEVMYPDIPLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADYAY 120 Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180 N +T +V LAH VG SVEGELGCLGSLETG GEAEDGHG E ALD S+LLTDPDEAA+ Sbjct: 121 NAMITTEVSRLAHMVGASVEGELGCLGSLETGHGEAEDGHGFEGALDRSQLLTDPDEAAR 180 Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240 FV T DALA+AIGTSHGAYKFTRKPTG++LA+D I+ IH+R+P TH+VMHGSSSVPQE Sbjct: 181 FVAETGVDALAVAIGTSHGAYKFTRKPTGEVLAMDVIEKIHERLPDTHIVMHGSSSVPQE 240 Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300 + +GG+++ETYGVPVEEI GIR+GVRKVNIDTD+RLA AA RRV +++EFD Sbjct: 241 WQDVFNAHGGEMRETYGVPVEEIVRGIRFGVRKVNIDTDLRLAAAAAFRRVADTSRTEFD 300 Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGEL 349 PRKF+ AM+ VC ARFEAFG+AG A +I+ + + EMA+RYASG L Sbjct: 301 PRKFLKPAMDAMSAVCKARFEAFGTAGNASRIKVVPMAEMARRYASGSL 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: 446 Number of extensions: 14 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: 354 Length of database: 359 Length adjustment: 29 Effective length of query: 325 Effective length of database: 330 Effective search space: 107250 Effective search space used: 107250 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 YP_001312666.1 Smed_3923 (fructose-1,6-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.30157.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-215 698.5 1.0 8.5e-215 698.3 1.0 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001312666.1 Smed_3923 fructose-1,6-bisphosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001312666.1 Smed_3923 fructose-1,6-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 698.3 1.0 8.5e-215 8.5e-215 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 698.3 bits; conditional E-value: 8.5e-215 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 +i+lrqlldhaaer+ygvpafn+nn+eq laimeaa+++d+pvilq+srgarsya++ +l+k+++a++ lcl|NCBI__GCF_000017145.1:YP_001312666.1 3 RITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARACDAPVILQVSRGARSYANDIMLAKMMEALEV 71 69******************************************************************* PP TIGR01521 70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138 +ypdip+++hqdhgn++atcl+aiq+gftsvmmdgslkedaktpady yn +t+ev++lah+vgasve lcl|NCBI__GCF_000017145.1:YP_001312666.1 72 MYPDIPLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADYAYNAMITTEVSRLAHMVGASVE 140 ********************************************************************* PP TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207 gelgclgsletg+geaedghgfegaldrsqlltdp+eaa+fv++t+vdalavaigtshgaykftrkptg lcl|NCBI__GCF_000017145.1:YP_001312666.1 141 GELGCLGSLETGHGEAEDGHGFEGALDRSQLLTDPDEAARFVAETGVDALAVAIGTSHGAYKFTRKPTG 209 ********************************************************************* PP TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276 evla+d+ie+iherlpdth+vmhgsssvpqew+dv+n++gge++etygvpveeiv+gi+fgvrkvnidt lcl|NCBI__GCF_000017145.1:YP_001312666.1 210 EVLAMDVIEKIHERLPDTHIVMHGSSSVPQEWQDVFNAHGGEMRETYGVPVEEIVRGIRFGVRKVNIDT 278 ********************************************************************* PP TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345 dlrlaa+aa+rrva+++++efdprkflk+a++am++vckar+eafgtagnas+ikvv++ emarrya+g lcl|NCBI__GCF_000017145.1:YP_001312666.1 279 DLRLAAAAAFRRVADTSRTEFDPRKFLKPAMDAMSAVCKARFEAFGTAGNASRIKVVPMAEMARRYASG 347 ********************************************************************* PP TIGR01521 346 el 347 +l lcl|NCBI__GCF_000017145.1:YP_001312666.1 348 SL 349 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (359 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: 6.99 // [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