Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_010626414.1 BZY95_RS21105 fructose-bisphosphate aldolase class II
Query= BRENDA::A0Q7I9 (354 letters) >NCBI__GCF_002151265.1:WP_010626414.1 Length = 354 Score = 582 bits (1499), Expect = e-171 Identities = 282/354 (79%), Positives = 317/354 (89%) Query: 1 MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60 MAL+S+RQ+LDHAAE GYG+PAFNVNNLEQ+RA+MEAAD +SPVI+Q SAGARKYAGA Sbjct: 1 MALISMRQMLDHAAERGYGIPAFNVNNLEQMRAIMEAADATDSPVIVQASAGARKYAGAP 60 Query: 61 FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120 F+RHL+LAA+EE+PHIPV MHQDHGTSP+VCQRSIQLGFSSVMMDGSL DGKTP DY+Y Sbjct: 61 FLRHLILAAVEEFPHIPVVMHQDHGTSPAVCQRSIQLGFSSVMMDGSLGEDGKTPMDYDY 120 Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180 NV+VT+ +MAHACGVSVEGELGCLGSLETG AGEEDGIGAEG LS DQLLTDPEEAA Sbjct: 121 NVDVTRRTVEMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLSHDQLLTDPEEAAA 180 Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240 FV+ T+VDALAIAIGTSHGAYKFTKPPTGD LSI+R+KEIHARIPDTHLVMHGSSSVPQ+ Sbjct: 181 FVKATQVDALAIAIGTSHGAYKFTKPPTGDTLSIQRIKEIHARIPDTHLVMHGSSSVPQE 240 Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300 WL VIN +GG + ETYGVPVEEIVE IKYGVRK+NIDTDLR+A+TGA+RRFLA++P EFD Sbjct: 241 WLAVINEFGGEIPETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAVRRFLAKHPGEFD 300 Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELDPIVK 354 PRKY AM +IC ARYEAFG+AG AS+IKPISLE M++RY GELDP VK Sbjct: 301 PRKYLKETVTAMRDICIARYEAFGTAGNASRIKPISLEAMYERYARGELDPKVK 354 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: 532 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 WP_010626414.1 BZY95_RS21105 (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.27416.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-211 685.4 0.1 8.2e-211 685.2 0.1 1.0 1 lcl|NCBI__GCF_002151265.1:WP_010626414.1 BZY95_RS21105 fructose-bisphosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_010626414.1 BZY95_RS21105 fructose-bisphosphate aldolase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 685.2 0.1 8.2e-211 8.2e-211 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 685.2 bits; conditional E-value: 8.2e-211 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 lis+rq+ldhaaergyg+pafnvnnleq++aimeaad+tdspvi+qas+gar+yag+++lr+l+laave lcl|NCBI__GCF_002151265.1:WP_010626414.1 3 LISMRQMLDHAAERGYGIPAFNVNNLEQMRAIMEAADATDSPVIVQASAGARKYAGAPFLRHLILAAVE 71 69******************************************************************* PP TIGR01521 70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138 e+p+ipvv+hqdhg+spa+c+++iqlgf+svmmdgsl ed+ktp dydynv+vt ++v++aha+g+sve lcl|NCBI__GCF_002151265.1:WP_010626414.1 72 EFPHIPVVMHQDHGTSPAVCQRSIQLGFSSVMMDGSLGEDGKTPMDYDYNVDVTRRTVEMAHACGVSVE 140 ********************************************************************* PP TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207 gelgclgsletg++++edg g+eg+l + qlltdpeeaa fvk t+vdala+aigtshgaykft++ptg lcl|NCBI__GCF_002151265.1:WP_010626414.1 141 GELGCLGSLETGMAGEEDGIGAEGVLSHDQLLTDPEEAAAFVKATQVDALAIAIGTSHGAYKFTKPPTG 209 ********************************************************************* PP TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276 ++l+i+ri+eih+r+pdthlvmhgsssvpqewl+vine+ggei+etygvpveeiv+gik+gvrkvnidt lcl|NCBI__GCF_002151265.1:WP_010626414.1 210 DTLSIQRIKEIHARIPDTHLVMHGSSSVPQEWLAVINEFGGEIPETYGVPVEEIVEGIKYGVRKVNIDT 278 ********************************************************************* PP TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345 dlrla+t+a+rr++ak+p efdprk+lk++v am+d+c+aryeafgtagnas+ik++sle m++rya+g lcl|NCBI__GCF_002151265.1:WP_010626414.1 279 DLRLASTGAVRRFLAKHPGEFDPRKYLKETVTAMRDICIARYEAFGTAGNASRIKPISLEAMYERYARG 347 ********************************************************************* PP TIGR01521 346 el 347 el lcl|NCBI__GCF_002151265.1:WP_010626414.1 348 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.55 // [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