Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_022949024.1 H035_RS0110990 fructose-bisphosphate aldolase class II
Query= BRENDA::Q602L6 (354 letters) >NCBI__GCF_000421465.1:WP_022949024.1 Length = 354 Score = 545 bits (1403), Expect = e-160 Identities = 264/354 (74%), Positives = 304/354 (85%) Query: 1 MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60 MALI+LRQLLDHAAE+GYG+PAFNVNNMEQ+ +IM+AAS VD+PVI+Q SAGAR YAGEP Sbjct: 1 MALITLRQLLDHAAENGYGVPAFNVNNMEQVHSIMDAASEVDSPVIMQASAGARKYAGEP 60 Query: 61 FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120 FLRHL+ AA+E +P +PV +HQDHGA P VC RSIQSGFSSVMMDGSL+ D KTPASY Y Sbjct: 61 FLRHLIVAALEQWPDVPVVLHQDHGADPGVCARSIQSGFSSVMMDGSLMPDAKTPASYEY 120 Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180 NVE T KVVEMAH+CGVSVEGELGCLGSLET +AGKEDG GAEG+L +LLTDP+EAAD Sbjct: 121 NVEVTAKVVEMAHSCGVSVEGELGCLGSLETMQAGKEDGVGAEGQLTKEMLLTDPNEAAD 180 Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240 FV++T+VDALAIAIGTSHGAYKFTR PTG +L IDR+K IH RIP HLVMHGSSSVP++ Sbjct: 181 FVKKTKVDALAIAIGTSHGAYKFTRPPTGDILAIDRIKEIHARIPDTHLVMHGSSSVPQD 240 Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300 W ++IN YGGD+GQTYGVPVEE+VEGI+HGVRKVNIDTDLR+AS GAMR+FM E+ K FD Sbjct: 241 WLEIINAYGGDMGQTYGVPVEEVVEGIKHGVRKVNIDTDLRMASTGAMRKFMAENPKQFD 300 Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354 PRK++ A AM IC+ARYEAFG AG +KIKP+ LED YA G+LDP VR Sbjct: 301 PRKIFAVATQAMKEICKARYEAFGCAGNGSKIKPINLEDTYKKYASGELDPKVR 354 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: 521 Number of extensions: 17 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_022949024.1 H035_RS0110990 (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.carbon/TIGR01521.hmm # target sequence database: /tmp/gapView.3694592.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-196 637.3 0.4 3.6e-196 637.1 0.4 1.0 1 NCBI__GCF_000421465.1:WP_022949024.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000421465.1:WP_022949024.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 637.1 0.4 3.6e-196 3.6e-196 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 637.1 bits; conditional E-value: 3.6e-196 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 li+lrqlldhaae+gygvpafnvnn+eq+ +im+aa + dspvi+qas+gar+yage++lr+l++aa e++pd NCBI__GCF_000421465.1:WP_022949024.1 3 LITLRQLLDHAAENGYGVPAFNVNNMEQVHSIMDAASEVDSPVIMQASAGARKYAGEPFLRHLIVAALEQWPD 75 69*********************************************************************** PP TIGR01521 74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146 +pvvlhqdhg++p +c ++iq gf+svmmdgsl daktpa+y+ynv+vta+vv++ah++g+svegelgclgs NCBI__GCF_000421465.1:WP_022949024.1 76 VPVVLHQDHGADPGVCARSIQSGFSSVMMDGSLMPDAKTPASYEYNVEVTAKVVEMAHSCGVSVEGELGCLGS 148 ************************************************************************* PP TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219 let ++++edg+g+eg+l + lltdp+eaa+fvkktkvdala+aigtshgaykftr+ptg++laidri+eih NCBI__GCF_000421465.1:WP_022949024.1 149 LETMQAGKEDGVGAEGQLTKEMLLTDPNEAADFVKKTKVDALAIAIGTSHGAYKFTRPPTGDILAIDRIKEIH 221 ************************************************************************* PP TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292 +r+pdthlvmhgsssvpq+wl++in+ygg++ +tygvpvee+v+gik+gvrkvnidtdlr+a+t+a+r+++a+ NCBI__GCF_000421465.1:WP_022949024.1 222 ARIPDTHLVMHGSSSVPQDWLEIINAYGGDMGQTYGVPVEEVVEGIKHGVRKVNIDTDLRMASTGAMRKFMAE 294 ************************************************************************* PP TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 +p++fdprk + a +amk++ckaryeafg agn skik+++le+ +++ya+gel NCBI__GCF_000421465.1:WP_022949024.1 295 NPKQFDPRKIFAVATQAMKEICKARYEAFGCAGNGSKIKPINLEDTYKKYASGEL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 19.76 // [ok]
This GapMind analysis is from Sep 24 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