Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate BWI76_RS23975 BWI76_RS23975 class II fructose-bisphosphate aldolase
Query= BRENDA::P0AB71 (359 letters) >FitnessBrowser__Koxy:BWI76_RS23975 Length = 359 Score = 695 bits (1794), Expect = 0.0 Identities = 337/359 (93%), Positives = 350/359 (97%) Query: 1 MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60 MSKIFDFVKPGVITGDDVQKVFQVAKEN FALPAVNCVGTDSINAVLE AAKV++PVIVQ Sbjct: 1 MSKIFDFVKPGVITGDDVQKVFQVAKENQFALPAVNCVGTDSINAVLEAAAKVRSPVIVQ 60 Query: 61 FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120 FSNGGA+FIAGKGVK+DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI Sbjct: 61 FSNGGAAFIAGKGVKTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120 Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180 DGLLDAGEKHFAATGKPLFSSHMIDLSEESL ENIEICSKYL RM+K+ MTLEIELGCTG Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLHENIEICSKYLARMAKMDMTLEIELGCTG 180 Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT Sbjct: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGS+AQEIKDSVSYGV+KMNIDTDTQWATW+G+ Sbjct: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSSAQEIKDSVSYGVIKMNIDTDTQWATWDGI 300 Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359 L YYK NEAYLQGQLGNPKGEDQPNKKYYDPRVWLRA QTSM+ RLE+AF+ELNAIDVL Sbjct: 301 LQYYKTNEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAAQTSMVTRLEQAFKELNAIDVL 359 Lambda K H 0.316 0.133 0.392 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: 583 Number of extensions: 5 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: 359 Length adjustment: 29 Effective length of query: 330 Effective length of database: 330 Effective search space: 108900 Effective search space used: 108900 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 BWI76_RS23975 BWI76_RS23975 (class II fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (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/TIGR01520.hmm # target sequence database: /tmp/gapView.20145.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01520 [M=357] Accession: TIGR01520 Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II 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-195 635.7 0.3 1.1e-195 635.5 0.3 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS23975 BWI76_RS23975 class II fructose- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS23975 BWI76_RS23975 class II fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 635.5 0.3 1.1e-195 1.1e-195 1 356 [. 4 358 .. 4 359 .] 0.99 Alignments for each domain: == domain 1 score: 635.5 bits; conditional E-value: 1.1e-195 TIGR01520 1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGv 71 ++d++k+gvi+g+dv+k+f+vake++fa+Pa+n+v+++++na+leaa++++sp+i+qfsnggaafiaGkGv lcl|FitnessBrowser__Koxy:BWI76_RS23975 4 IFDFVKPGVITGDDVQKVFQVAKENQFALPAVNCVGTDSINAVLEAAAKVRSPVIVQFSNGGAAFIAGKGV 74 6899******************************************************************* PP TIGR01520 72 kdeaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmld 142 k++++++a+i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+d lcl|FitnessBrowser__Koxy:BWI76_RS23975 75 KTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMID 145 *********************************************************************** PP TIGR01520 143 lseepieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispk 213 lsee+++eniei++kyl rmak++++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y+elskisp+ lcl|FitnessBrowser__Koxy:BWI76_RS23975 146 LSEESLHENIEICSKYLARMAKMDMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPR 216 *********************************************************************** PP TIGR01520 214 fsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkv 284 f+iaa+fGnvhGvykpGnv+l+P+il+d+qeyv++k++l+ +++l+fvfhGGsGs+++eik+++syGv+k+ lcl|FitnessBrowser__Koxy:BWI76_RS23975 217 FTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVSKKHNLP-HNSLNFVFHGGSGSSAQEIKDSVSYGVIKM 286 ****************************************.9***************************** PP TIGR01520 285 nvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnain 355 n+dtdtq+a++ gil+y+++ne+ylq+q+Gnpkge++pnkk+ydPrvwlr+a++sm r+e+a++elnai+ lcl|FitnessBrowser__Koxy:BWI76_RS23975 287 NIDTDTQWATWDGILQYYKTNEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAAQTSMVTRLEQAFKELNAID 357 *********************************************************************98 PP TIGR01520 356 k 356 + lcl|FitnessBrowser__Koxy:BWI76_RS23975 358 V 358 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (359 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: 9.27 // [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