Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate AZOBR_RS30885 AZOBR_RS30885 fructose-bisphosphate aldolase
Query= BRENDA::A0KGD4 (359 letters) >FitnessBrowser__azobra:AZOBR_RS30885 Length = 359 Score = 396 bits (1018), Expect = e-115 Identities = 204/350 (58%), Positives = 259/350 (74%), Gaps = 7/350 (2%) Query: 9 VKPGVITGDDVQKVFAIAKENGFALPAVNCVGTDSVNAVLEAAAKVKAPVIVQFSNGGAV 68 +KPGV+TG+D + + A ++ G+ALPAVN VGT+ +NAVLEAAAK ++ VIVQ SNGGA Sbjct: 7 LKPGVVTGEDYRALIAACQDGGYALPAVNVVGTNGINAVLEAAAKNRSDVIVQLSNGGAR 66 Query: 69 FTAGKGLKLEGQQAAIIGAISGAKHVHAVAEAYGVPVILHTDHAAKKLLPWIDGLLDAGE 128 F AG+G+K + QA I+GA+S A+HVH +AE YGV V+LHTDHA K L+PW++G++D GE Sbjct: 67 FYAGEGMK-DALQARILGAVSAAQHVHLLAEQYGVCVVLHTDHANKGLIPWVEGMIDHGE 125 Query: 129 KHFAETGKPLFSSHMLDLSEESLEENIDICCEYLTRMAKMNMTLELELGCTGGEEDGVDN 188 +HF TG+PLFSSHMLDLSEESL+ N+ C L R+A + M+LE+ELG TGGEEDG+ + Sbjct: 126 EHFRRTGRPLFSSHMLDLSEESLDFNLSECARVLKRLAPLGMSLEIELGVTGGEEDGIGS 185 Query: 189 SHMD---QSALYTQPEDVAYAYERLSKISPRFTIAASFGNVHGVYKPGNVKLTPSILDAS 245 +D + LYTQPEDV AYE LS I F++AASFGNVHGVY PGNVKL P IL AS Sbjct: 186 EDLDAANNAHLYTQPEDVLRAYEELSPIG-HFSVAASFGNVHGVYAPGNVKLRPEILGAS 244 Query: 246 QKYVSEKFGIPAKSLDFVFHGGSGSTLEEIRESISYGVVKMNIDTDTQWATWEGILGFYK 305 Q V+E+ G AK L VFHGGSGS E+I +++ +GV KMNIDTDTQ+A E I GF Sbjct: 245 QALVAERHGGGAKPLALVFHGGSGSEKEKIAQAVGFGVFKMNIDTDTQFAFAESIGGFVL 304 Query: 306 KNEAYLQGQLGNPEGADKPNKKFYDPRVWLRAGQTTMIARLEKAFSDLNA 355 +NEA + Q+ G KP KK YDPR WLR G+ M+ RL++AF+DL A Sbjct: 305 ENEAAFRHQIDPQSG--KPLKKLYDPRKWLRLGEQGMVRRLDEAFADLGA 352 Lambda K H 0.316 0.134 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: 372 Number of extensions: 9 Number of successful extensions: 5 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 AZOBR_RS30885 AZOBR_RS30885 (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.aa/TIGR01520.hmm # target sequence database: /tmp/gapView.19528.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-139 450.1 0.0 3.4e-139 449.7 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS30885 AZOBR_RS30885 fructose-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS30885 AZOBR_RS30885 fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.7 0.0 3.4e-139 3.4e-139 4 356 .. 6 355 .. 4 356 .. 0.96 Alignments for each domain: == domain 1 score: 449.7 bits; conditional E-value: 3.4e-139 TIGR01520 4 klktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvk 72 lk+gv++ged++ l+ +++ +a+Pa+nvv+++ +na+leaa++ +s++i+q+sngga f+aG G+k lcl|FitnessBrowser__azobra:AZOBR_RS30885 6 RLKPGVVTGEDYRALIAACQDGGYALPAVNVVGTNGINAVLEAAAKNRSDVIVQLSNGGARFYAGEGMK 74 5799***************************************************************** PP TIGR01520 73 deaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshml 141 d a +a i Ga++aa++v+ +ae+ygv vvlhtdh k l+p+v+g+++++e++f+++g+Plfsshml lcl|FitnessBrowser__azobra:AZOBR_RS30885 75 D-ALQA-RILGAVSAAQHVHLLAEQYGVCVVLHTDHANKGLIPWVEGMIDHGEEHFRRTGRPLFSSHML 141 9.5566.7************************************************************* PP TIGR01520 142 dlseepieenieiakkylkrmakiklileieiGitGGeedGvdneead...keelytkPedvekvyeel 207 dlsee+++ n++ + + lkr+a++ + leie+G+tGGeedG+ e+ d +++lyt+Pedv ++yeel lcl|FitnessBrowser__azobra:AZOBR_RS30885 142 DLSEESLDFNLSECARVLKRLAPLGMSLEIELGVTGGEEDGIGSEDLDaanNAHLYTQPEDVLRAYEEL 210 ******************************************998866222678*************** PP TIGR01520 208 skispkfsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikea 276 s+i ++fs+aa+fGnvhGvy+pGnvklrP+il +q+ vae++g akpl +vfhGGsGs ke i +a lcl|FitnessBrowser__azobra:AZOBR_RS30885 211 SPI-GHFSVAASFGNVHGVYAPGNVKLRPEILGASQALVAERHGGG-AKPLALVFHGGSGSEKEKIAQA 277 **9.79**************************************99.9********************* PP TIGR01520 277 lsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarve 345 + +Gv k+n+dtdtq+a+ e+i ++vl+ne+ ++q+ p + kp kk ydPr wlr +e+ m r+ lcl|FitnessBrowser__azobra:AZOBR_RS30885 278 VGFGVFKMNIDTDTQFAFAESIGGFVLENEAAFRHQID-P-QSGKPLKKLYDPRKWLRLGEQGMVRRLD 344 ************************************98.4.5679************************ PP TIGR01520 346 kaleelnaink 356 +a+ +l a++k lcl|FitnessBrowser__azobra:AZOBR_RS30885 345 EAFADLGAAGK 355 ****9988765 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.77 // [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