Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 200117 SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file)
Query= BRENDA::A0Q7I9 (354 letters) >FitnessBrowser__MR1:200117 Length = 355 Score = 542 bits (1397), Expect = e-159 Identities = 258/351 (73%), Positives = 306/351 (87%) Query: 1 MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60 MAL+SLRQLLDHAAEHGYG+PAFNVNNLEQ+RA+M+AA+ +SPVI+Q SAGARKYA Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60 Query: 61 FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120 F+++L+ AA+E+YP IPVC+HQDHGT P +CQRSIQLG SSVMMDGSL +DGKTPA YEY Sbjct: 61 FLKYLMTAALEQYPDIPVCIHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEY 120 Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180 NV+VT+ AHACGVSVEGE+GCLGSLETG AGEEDG+GAEG LS DQLLT PEEAA Sbjct: 121 NVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGVGAEGVLSHDQLLTSPEEAAR 180 Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240 FV T VDALAIAIGTSHGAYKF++ PTGDVL I R+KEIHARIP+THLVMHGSSSVPQ+ Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240 Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300 WL++IN YGG + ETYGVP+EEIVE IK+GVRK+NIDTDLR+A+TGA+R++LAE+P+EFD Sbjct: 241 WLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFD 300 Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELDP 351 PRK+ + AM++IC RYEAFG AG ASKIKP+SL+ M++ Y+SG LDP Sbjct: 301 PRKFLKASMEAMADICTVRYEAFGCAGQASKIKPLSLQAMYKAYQSGALDP 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: 524 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: 355 Length adjustment: 29 Effective length of query: 325 Effective length of database: 326 Effective search space: 105950 Effective search space used: 105950 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 200117 SO0933 (fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file))
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.10225.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-196 638.0 0.1 2.2e-196 637.8 0.1 1.0 1 lcl|FitnessBrowser__MR1:200117 SO0933 fructose-bisphosphate ald Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200117 SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 637.8 0.1 2.2e-196 2.2e-196 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 637.8 bits; conditional E-value: 2.2e-196 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvvlh 79 lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya ++l+ l+ aa e+ypdipv++h lcl|FitnessBrowser__MR1:200117 3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMTAALEQYPDIPVCIH 81 69***************************************************************************** PP TIGR01521 80 qdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgeaedgh 158 qdhg++p++c+++iqlg++svmmdgsl +d+ktpa+y+ynv+vt ++v++aha+g+svege+gclgsletg++++edg+ lcl|FitnessBrowser__MR1:200117 82 QDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEYNVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGV 160 ******************************************************************************* PP TIGR01521 159 gfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhgsssvpq 237 g+eg+l + qllt peeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhgsssvpq lcl|FitnessBrowser__MR1:200117 161 GAEGVLSHDQLLTSPEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQ 239 ******************************************************************************* PP TIGR01521 238 ewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvcka 316 ewl++in+ygg+i+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+ +a++psefdprkflk ++eam d+c+ lcl|FitnessBrowser__MR1:200117 240 EWLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFDPRKFLKASMEAMADICTV 318 ******************************************************************************* PP TIGR01521 317 ryeafgtagnaskikvvsleemarryakgel 347 ryeafg ag+askik++sl+ m++ y +g l lcl|FitnessBrowser__MR1:200117 319 RYEAFGCAGQASKIKPLSLQAMYKAYQSGAL 349 ***************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (355 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.03 // [ok]
This GapMind analysis is from Apr 09 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