Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate Ac3H11_686 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
Query= BRENDA::Q9K1F1 (269 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_686 Length = 279 Score = 317 bits (811), Expect = 2e-91 Identities = 159/267 (59%), Positives = 202/267 (75%), Gaps = 1/267 (0%) Query: 2 TPLKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGLKTGIAISD 61 TP ++A+AGA+GRMGR+L+EA+ D VL+GAL+ + S A+G DA +G +G+AI+ Sbjct: 13 TPCRVAVAGASGRMGRMLIEAIRASDDCVLAGALDVAASPAVGSDATAFLGHASGVAITA 72 Query: 62 DVDAVLAQSDVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTGIV 121 D+ A L +DVLIDFTRPE TL HL C + V +IGTTGF D KA + A++T I+ Sbjct: 73 DIAAGLKNADVLIDFTRPEGTLAHLAVCSQLGVKAVIGTTGFTDAQKAELDACAQRTAIM 132 Query: 122 FAANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIAGALGR 181 F+ N SVGVN+T +L A+ + GYDIEIIE HHRHKVDAPSGTAL+MGEVIA A+GR Sbjct: 133 FSPNMSVGVNVTLKLLQMAAKAMTTGYDIEIIEAHHRHKVDAPSGTALKMGEVIAEAMGR 192 Query: 182 DLKQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMTFA 241 DLK+CAVY REG TG RDPS+IGFA +R GDIVGDHT LFA GER+E+THK+SSR T+A Sbjct: 193 DLKECAVYAREGVTGERDPSSIGFAAIRGGDIVGDHTVLFAGIGERIEVTHKSSSRATYA 252 Query: 242 AGAVRAAVWVNG-KTGLYDMQDVLGLN 267 GA+RA ++ KTG++DM DVLGL+ Sbjct: 253 QGALRAVRFLAAHKTGMFDMFDVLGLH 279 Lambda K H 0.318 0.136 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: 295 Number of extensions: 8 Number of successful extensions: 2 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: 269 Length of database: 279 Length adjustment: 25 Effective length of query: 244 Effective length of database: 254 Effective search space: 61976 Effective search space used: 61976 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate Ac3H11_686 (4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
# 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/TIGR00036.hmm # target sequence database: /tmp/gapView.29746.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00036 [M=270] Accession: TIGR00036 Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-99 318.5 3.6 2.2e-99 318.4 3.6 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.4 3.6 2.2e-99 2.2e-99 3 270 .] 16 277 .. 14 277 .. 0.98 Alignments for each domain: == domain 1 score: 318.4 bits; conditional E-value: 2.2e-99 TIGR00036 3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleav 65 +vavaGa+GrmGr +i+a+ +++d l++al++ +s+ +g+D+ + g ++ gv++++d+ a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 16 RVAVAGASGRMGRMLIEAIRASDDCVLAGALDVAASPAVGSDATAFLGHAS-GVAITADIAAG 77 8**********************************************9876.8999***9988 PP TIGR00036 66 kvlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalvia 128 k+advliDft+pe++l +++++ + gv+ V+GTTGf++++++el ++a++ +a++++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 78 ----LKNADVLIDFTRPEGTLAHLAVCSQLGVKAVIGTTGFTDAQKAELDACAQR--TAIMFS 134 ....899************************************************..****** PP TIGR00036 129 pNfaiGvnlllkllekaakvled.vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkea 190 pN+++Gvn+ lkll++aak ++ +DiEiiE+HHrhK+DaPSGTAlk++e+ia+a g+dlke+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 135 PNMSVGVNVTLKLLQMAAKAMTTgYDIEIIEAHHRHKVDAPSGTALKMGEVIAEAMGRDLKEC 197 *******************997627************************************** PP TIGR00036 191 aveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrair 253 av+ reg+tGer ++iG+aa+Rggd+vg+htvlFa++Ger+e+tHk+ssRa++a+G++ra+r lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 198 AVYAREGVTGERDPSSIGFAAIRGGDIVGDHTVLFAGIGERIEVTHKSSSRATYAQGALRAVR 260 *************************************************************** PP TIGR00036 254 wledkeekvydledvld 270 +l+ +++++d+ dvl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_686 261 FLAAHKTGMFDMFDVLG 277 ***************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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: 8.77 // [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