Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_025331513.1 SALWKB2_RS09870 fructose-bisphosphate aldolase class II
Query= BRENDA::Q602L6 (354 letters) >NCBI__GCF_000600005.1:WP_025331513.1 Length = 354 Score = 509 bits (1310), Expect = e-149 Identities = 251/354 (70%), Positives = 294/354 (83%) Query: 1 MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60 MAL+S+RQLLDHAAE+ YGLPAFNVNN+EQ++AIMEAA V+APVI+Q SAGAR YAG P Sbjct: 1 MALVSMRQLLDHAAENSYGLPAFNVNNLEQMRAIMEAADEVNAPVIVQASAGARKYAGAP 60 Query: 61 FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120 FLRHL+ AAIE +PHIPV MHQDHGASP VC RSIQ GFSSVMMDGSLL D KTP++Y Y Sbjct: 61 FLRHLILAAIEEFPHIPVVMHQDHGASPEVCQRSIQLGFSSVMMDGSLLSDAKTPSTYEY 120 Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180 NV+ TRK V MAHACGVSVEGE+GCLG+LETG AG+EDG GA G+L H +LT DEAA Sbjct: 121 NVDVTRKTVYMAHACGVSVEGEIGCLGNLETGDAGEEDGVGAAGKLSHEQMLTSVDEAAR 180 Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240 FV+ T VDALAIAIGTSHGAYKFTRKPTG+VLRIDR++ IH+R+P HLVMHGSSSVP+E Sbjct: 181 FVQDTGVDALAIAIGTSHGAYKFTRKPTGEVLRIDRIREIHERLPNTHLVMHGSSSVPQE 240 Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300 W Q+IN++GG+I +TYGVPVEEIVEGI++GVRKVNIDTDLR+AS GA+RRF+ FD Sbjct: 241 WLQVINEFGGNIPETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIRRFLATHPAEFD 300 Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354 PRK + AM +C RY AFGAAG A++IKP+ LE M+ YA G+L IV+ Sbjct: 301 PRKYFTETIKAMKQVCIDRYVAFGAAGHASQIKPISLEKMANRYAAGELVQIVK 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: 493 Number of extensions: 13 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_025331513.1 SALWKB2_RS09870 (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.1531118.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-199 647.0 0.3 4e-199 646.8 0.3 1.0 1 NCBI__GCF_000600005.1:WP_025331513.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000600005.1:WP_025331513.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.8 0.3 4e-199 4e-199 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 646.8 bits; conditional E-value: 4e-199 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 l+s+rqlldhaae++yg+pafnvnnleq++aimeaad+ ++pvi+qas+gar+yag+++lr+l+laa+ee+p+ NCBI__GCF_000600005.1:WP_025331513.1 3 LVSMRQLLDHAAENSYGLPAFNVNNLEQMRAIMEAADEVNAPVIVQASAGARKYAGAPFLRHLILAAIEEFPH 75 69*********************************************************************** PP TIGR01521 74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146 ipvv+hqdhg+sp++c+++iqlgf+svmmdgsl daktp+ y+ynv+vt ++v +aha+g+svege+gclg NCBI__GCF_000600005.1:WP_025331513.1 76 IPVVMHQDHGASPEVCQRSIQLGFSSVMMDGSLLSDAKTPSTYEYNVDVTRKTVYMAHACGVSVEGEIGCLGN 148 ************************************************************************* PP TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219 letg +++edg+g+ g+l + q+lt +eaa+fv++t+vdala+aigtshgaykftrkptgevl idri+eih NCBI__GCF_000600005.1:WP_025331513.1 149 LETGDAGEEDGVGAAGKLSHEQMLTSVDEAARFVQDTGVDALAIAIGTSHGAYKFTRKPTGEVLRIDRIREIH 221 ************************************************************************* PP TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292 erlp+thlvmhgsssvpqewl+vine+gg+i+etygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a+ NCBI__GCF_000600005.1:WP_025331513.1 222 ERLPNTHLVMHGSSSVPQEWLQVINEFGGNIPETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIRRFLAT 294 ************************************************************************* PP TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 +p efdprk++ ++++amk+vc++ry afg+ag as+ik++sle+ma+rya gel NCBI__GCF_000600005.1:WP_025331513.1 295 HPAEFDPRKYFTETIKAMKQVCIDRYVAFGAAGHASQIKPISLEKMANRYAAGEL 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: 26.53 // [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