Align Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate WP_008807883.1 KVAR_RS25120 rhamnulose-1-phosphate aldolase
Query= reanno::Koxy:BWI76_RS00670 (276 letters) >NCBI__GCF_000025465.1:WP_008807883.1 Length = 276 Score = 545 bits (1404), Expect = e-160 Identities = 267/275 (97%), Positives = 267/275 (97%) Query: 1 MQTIIDAWFVQGMIKATSDAWLKGWDERNGGNLTLRLDEADIEPYAADFHAKPRYIALSQ 60 MQTIIDAWFVQGMIKATSDAWLKGWDERNGGNLTLRLDEADIEPYAADFHAKPRYIALSQ Sbjct: 1 MQTIIDAWFVQGMIKATSDAWLKGWDERNGGNLTLRLDEADIEPYAADFHAKPRYIALSQ 60 Query: 61 PMPTLANQPFIVTGSGKFFRNVQLDPAANLGVVKVDSDGAGYHILWGLTNDAVPTSELPA 120 PMP LANQPFIVTGSGKFFRNVQLDPAANLGVVKVDSDGAGYHILWGLT DAVPTSELPA Sbjct: 61 PMPILANQPFIVTGSGKFFRNVQLDPAANLGVVKVDSDGAGYHILWGLTEDAVPTSELPA 120 Query: 121 HFLSHSERIKLTNGKDRVIMHCHATNLIALTYVLENSSDLFTRKLWEGSTECLVVFPDGV 180 HFLSHSERIKLT GKDRVIMHCHATNLIALTYVLEN SDLFTRKLWEGSTECLVVFPDGV Sbjct: 121 HFLSHSERIKLTGGKDRVIMHCHATNLIALTYVLENHSDLFTRKLWEGSTECLVVFPDGV 180 Query: 181 GILPWMVPGTDEIGQATAEAMQKHSLVLWPFHGVFGSGPNLDETFGLIDTAEKSAEVLVK 240 GILPWMVPGTDEIGQATAE MQKHSLVLWPFHGVFGSGP LDETFGLIDTAEKSAEVLVK Sbjct: 181 GILPWMVPGTDEIGQATAETMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAEVLVK 240 Query: 241 VYSMGGMKQTITREELIALGKRFNVHPLQSALDLY 275 V SMGGMKQTITREELIALGKRFNV PLQSALDLY Sbjct: 241 VLSMGGMKQTITREELIALGKRFNVQPLQSALDLY 275 Lambda K H 0.319 0.136 0.420 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: 382 Number of extensions: 6 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 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: 47 (22.7 bits)
Align candidate WP_008807883.1 KVAR_RS25120 (rhamnulose-1-phosphate aldolase)
to HMM TIGR02624 (rhaD: rhamnulose-1-phosphate aldolase (EC 4.1.2.19))
# 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/TIGR02624.hmm # target sequence database: /tmp/gapView.22092.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02624 [M=270] Accession: TIGR02624 Description: rhamnu_1P_ald: rhamnulose-1-phosphate aldolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-140 451.4 0.0 5.7e-140 451.2 0.0 1.0 1 lcl|NCBI__GCF_000025465.1:WP_008807883.1 KVAR_RS25120 rhamnulose-1-phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_008807883.1 KVAR_RS25120 rhamnulose-1-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.2 0.0 5.7e-140 5.7e-140 1 270 [] 1 272 [. 1 272 [. 0.99 Alignments for each domain: == domain 1 score: 451.2 bits; conditional E-value: 5.7e-140 TIGR02624 1 mqdildavfvkemikttedlyrkGwdernGGnislrlkeeeveayld.lkqvlrkiplkfdakelanky 68 mq i+da+fv++mik+t+d++ kGwdernGGn++lrl+e+++e+y+ ++ +r+i l+++++ lan+ lcl|NCBI__GCF_000025465.1:WP_008807883.1 1 MQTIIDAWFVQGMIKATSDAWLKGWDERNGGNLTLRLDEADIEPYAAdFHAKPRYIALSQPMPILANQP 69 789******************************************876********************* PP TIGR02624 69 flvtGsGkyfknveeapaenlgllrvsedGksvellwGltdgglptselpahflshiarlkvdp.enrv 136 f+vtGsGk+f+nv+ +pa+nlg+++v++dG+ +++lwGlt++++ptselpahflsh +r+k ++ ++rv lcl|NCBI__GCF_000025465.1:WP_008807883.1 70 FIVTGSGKFFRNVQLDPAANLGVVKVDSDGAGYHILWGLTEDAVPTSELPAHFLSHSERIKLTGgKDRV 138 *************************************************************9998**** PP TIGR02624 137 imhchatnlialtftleldekaftrtlwemsteclvvfpeGvGiipwlvpGtdeiGeataekmkesrlv 205 imhchatnlialt++le+++ ftr+lwe+steclvvfp+GvGi+pw+vpGtdeiG+atae m++++lv lcl|NCBI__GCF_000025465.1:WP_008807883.1 139 IMHCHATNLIALTYVLENHSDLFTRKLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAETMQKHSLV 207 ********************************************************************* PP TIGR02624 206 lwphhGifgaGesldevfGlietaekaaevytkvlsqggvkqtisdedlialaerfdvkpkakyl 270 lwp+hG+fg+G++lde+fGli+taek+aev++kvls+gg+kqti++e+lial++rf+v+p +++l lcl|NCBI__GCF_000025465.1:WP_008807883.1 208 LWPFHGVFGSGPTLDETFGLIDTAEKSAEVLVKVLSMGGMKQTITREELIALGKRFNVQPLQSAL 272 ************************************************************98875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (276 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.87 // [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