Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)
Query= BRENDA::Q602L6 (354 letters) >FitnessBrowser__SB2B:6938653 Length = 355 Score = 504 bits (1297), Expect = e-147 Identities = 249/351 (70%), Positives = 284/351 (80%) Query: 1 MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60 MALISLRQLLDHAAEHGYG+PAFNVNN+EQ++AIM+AA A D+PVI+Q SAGAR YA Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60 Query: 61 FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120 FL++L+ AA+E YP IPVC+HQDHG P VC RSIQ G SSVMMDGSL+ D KTPASY Y Sbjct: 61 FLKYLMNAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDY 120 Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180 NV+ TRK V AHACGVSVEGE+GCLGSLETG AG+EDG GA G L H LLT +EAA Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGIGAVGVLSHDQLLTTAEEAAR 180 Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240 FV T VDALAIAIGTSHGAYKF+RKPTG VLRIDR+K IH RIP HLVMHGSSSVP+ Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQY 240 Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300 W ++IN YGG+I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+F+ E+ FD Sbjct: 241 WLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300 Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDP 351 PRK KA+ AM IC RYEAFG AG A+KIKPL L+ M Y G+LDP Sbjct: 301 PRKFLKASMEAMADICTERYEAFGCAGMASKIKPLSLQAMYKRYQTGELDP 351 Lambda K H 0.320 0.134 0.391 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: 486 Number of extensions: 18 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate 6938653 Sama_2756 (fructose-1,6-bisphosphate aldolase (RefSeq))
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.carbon/TIGR01521.hmm # target sequence database: /tmp/gapView.19928.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-195 634.1 0.2 3.3e-195 633.9 0.2 1.0 1 lcl|FitnessBrowser__SB2B:6938653 Sama_2756 fructose-1,6-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 633.9 0.2 3.3e-195 3.3e-195 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 633.9 bits; conditional E-value: 3.3e-195 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvv 77 lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya ++l+ l+ aa e+ypdipv+ lcl|FitnessBrowser__SB2B:6938653 3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMNAALEQYPDIPVC 79 69*************************************************************************** PP TIGR01521 78 lhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgea 154 +hqdhg+ p++c+++iqlg++svmmdgsl d+ktpa+ydynv+vt ++v++aha+g+svege+gclgsletg++++ lcl|FitnessBrowser__SB2B:6938653 80 IHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDYNVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGE 156 ***************************************************************************** PP TIGR01521 155 edghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhg 231 edg g+ g+l + qllt eeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhg lcl|FitnessBrowser__SB2B:6938653 157 EDGIGAVGVLSHDQLLTTAEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHG 233 ***************************************************************************** PP TIGR01521 232 sssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkave 308 sssvpq wl++in+yggei+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+++a++psefdprkflk ++e lcl|FitnessBrowser__SB2B:6938653 234 SSSVPQYWLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFDPRKFLKASME 310 ***************************************************************************** PP TIGR01521 309 amkdvckaryeafgtagnaskikvvsleemarryakgel 347 am d+c++ryeafg ag askik++sl+ m++ry gel lcl|FitnessBrowser__SB2B:6938653 311 AMADICTERYEAFGCAGMASKIKPLSLQAMYKRYQTGEL 349 *************************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.34 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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