Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_012335659.1 M446_RS29000 class II fructose-bisphosphate aldolase
Query= SwissProt::Q8YNK2 (359 letters) >NCBI__GCF_000019365.1:WP_012335659.1 Length = 362 Score = 474 bits (1221), Expect = e-138 Identities = 240/362 (66%), Positives = 287/362 (79%), Gaps = 4/362 (1%) Query: 1 MALVPLRLLLDHAAENGYGIPAFNVNNLEQIQAILKAAAETDSPVILQASRGARNYAGEN 60 MA + LR LLDHAAE+GYG+PAFN+NN+EQ AI+ AA TDSPVILQASRGAR YA + Sbjct: 1 MARITLRQLLDHAAEHGYGVPAFNINNMEQGLAIMAAADATDSPVILQASRGARAYANDV 60 Query: 61 FLRHLILAAVETYPEIPIVMHQDHGNAPSTCYSAIKNNFTSVMMDGSLEADAKTPASFEY 120 L LI VE YP IP+ MH DHGN +TC +AI+ FTSVMMDGSL+AD KTPA + Y Sbjct: 61 VLAKLIDGLVEIYPHIPVCMHLDHGNNEATCATAIQYGFTSVMMDGSLKADGKTPADYAY 120 Query: 121 NVNVTREVVNVAHALGVSVEGELGCLGSLETGAGEAEDGHGFEGTLDHSQLLTDPDEAVN 180 NV +TR+V +AH GVSVEGELG LGSLE+G GEAEDGHG EGTL H QLLTDP+EAV Sbjct: 121 NVEITRKVAEMAHWAGVSVEGELGVLGSLESGQGEAEDGHGAEGTLSHDQLLTDPEEAVK 180 Query: 181 FVEATQVDALAVAIGTSHGAYKFTRKPTGEILAISRIEEIHRRLPNTHLVMHGSSSVPED 240 FVEAT+VDALAVA+GTSHGAYKFTRKP G +LA+ IEEI+RRLPNTHLVMHGSSSVP+D Sbjct: 181 FVEATKVDALAVAMGTSHGAYKFTRKPDGAVLAMHVIEEINRRLPNTHLVMHGSSSVPQD 240 Query: 241 LIALINEYGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAVREALAKNPKEFD 300 L +IN+YGG + T+GVPVEEIQ+GIK GVRK+NIDTDNR+A+T +R+ LA+N EFD Sbjct: 241 LQDIINQYGGEMKPTWGVPVEEIQRGIKHGVRKINIDTDNRMAMTGQIRKVLAENKAEFD 300 Query: 301 PRHFLKPSITYMQKVCAERYVQFGTAGNASKIKQVSLETFAAKYAKGELN----AISKAA 356 PR +LKP++ M K+C +R+ +FGTAG A KI+ VSL A +YA G+L+ A KAA Sbjct: 301 PRKYLKPAMDAMTKLCKQRFEEFGTAGQAGKIRPVSLSEMAKRYAAGKLDPSFGATRKAA 360 Query: 357 AK 358 A+ Sbjct: 361 AE 362 Lambda K H 0.315 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: 495 Number of extensions: 20 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: 359 Length of database: 362 Length adjustment: 29 Effective length of query: 330 Effective length of database: 333 Effective search space: 109890 Effective search space used: 109890 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_012335659.1 M446_RS29000 (class II 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.885858.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-192 625.8 0.8 1.1e-192 625.6 0.8 1.0 1 NCBI__GCF_000019365.1:WP_012335659.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019365.1:WP_012335659.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 625.6 0.8 1.1e-192 1.1e-192 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 625.6 bits; conditional E-value: 1.1e-192 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 +i+lrqlldhaae+gygvpafn+nn+eq laim aad+tdspvilqasrgar ya++v+l+kl+ ++ve yp+ NCBI__GCF_000019365.1:WP_012335659.1 3 RITLRQLLDHAAEHGYGVPAFNINNMEQGLAIMAAADATDSPVILQASRGARAYANDVVLAKLIDGLVEIYPH 75 69*********************************************************************** PP TIGR01521 74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146 ipv++h dhgn+ atc +aiq gftsvmmdgslk+d+ktpady ynv++t +v+++ah g+svegelg lgs NCBI__GCF_000019365.1:WP_012335659.1 76 IPVCMHLDHGNNEATCATAIQYGFTSVMMDGSLKADGKTPADYAYNVEITRKVAEMAHWAGVSVEGELGVLGS 148 ************************************************************************* PP TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219 le+g+geaedghg+eg+l + qlltdpeea++fv+ tkvdalava+gtshgaykftrkp g vla+++ieei NCBI__GCF_000019365.1:WP_012335659.1 149 LESGQGEAEDGHGAEGTLSHDQLLTDPEEAVKFVEATKVDALAVAMGTSHGAYKFTRKPDGAVLAMHVIEEIN 221 ************************************************************************* PP TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292 +rlp+thlvmhgsssvpq+ +d+in+ygge+k t+gvpveei++gik+gvrk+nidtd+r+a+t+ +r+v+a+ NCBI__GCF_000019365.1:WP_012335659.1 222 RRLPNTHLVMHGSSSVPQDLQDIINQYGGEMKPTWGVPVEEIQRGIKHGVRKINIDTDNRMAMTGQIRKVLAE 294 ************************************************************************* PP TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 ++ efdprk+lk+a++am ++ck+r+e+fgtag+a ki++vsl ema+rya g+l NCBI__GCF_000019365.1:WP_012335659.1 295 NKAEFDPRKYLKPAMDAMTKLCKQRFEEFGTAGQAGKIRPVSLSEMAKRYAAGKL 349 ****************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (362 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.17 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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