Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate N515DRAFT_2721 N515DRAFT_2721 dihydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >FitnessBrowser__Dyella79:N515DRAFT_2721 Length = 266 Score = 204 bits (519), Expect = 2e-57 Identities = 120/263 (45%), Positives = 162/263 (61%), Gaps = 9/263 (3%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 +R+A+ GA GRMGR L+ L + + A+ SS LG E AG+ G+ Sbjct: 5 LRLAVIGATGRMGRALLD--LLKDDARFELAVALAASSRLG----EPVYAGEDGLRFTRE 58 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 A + V IDF+ P G LA CR H +V GTTG D+A +Q + +AA DI ++ Sbjct: 59 WPAAAPE--VAIDFSGPAGLGAALAHCRAHRIALVTGTTGLDQALQQQLDEAARDIPLLR 116 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 AANFS+GV V+ +L+ +AA + D+ D++I+EAHH KVDAPSGTALA+GEA A Sbjct: 117 AANFSLGVAVLRRLVRQAAAALPDW-DLDILEAHHNRKVDAPSGTALALGEAAAAGRGVS 175 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 L D AVY+REG TG R G+IGFA VR GDIVGEH GER+E+ H+A+ R FA Sbjct: 176 LADGAVYAREGTTGPRQHGSIGFAVVRGGDIVGEHEVWVIGPGERVELNHRATDRSIFAR 235 Query: 246 GAVRSALWLSGKESGLFDMRDVL 268 GA+ +A WL+G+ G +D+ +L Sbjct: 236 GAIEAAHWLAGRAPGAYDLDAML 258 Lambda K H 0.319 0.135 0.383 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: 250 Number of extensions: 13 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: 273 Length of database: 266 Length adjustment: 25 Effective length of query: 248 Effective length of database: 241 Effective search space: 59768 Effective search space used: 59768 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 N515DRAFT_2721 N515DRAFT_2721 (dihydrodipicolinate reductase)
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.17650.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-72 230.5 0.0 1.9e-72 230.0 0.0 1.2 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 N515DRAFT_2721 dihydrodipicolina Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 N515DRAFT_2721 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 230.0 0.0 1.9e-72 1.9e-72 2 269 .. 5 258 .. 4 259 .. 0.97 Alignments for each domain: == domain 1 score: 230.0 bits; conditional E-value: 1.9e-72 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkv 67 +++av Ga+GrmGr ++ +k+ +el+ al + ss+ +Ge + +g+ g+ + + a+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 5 LRLAVIGATGRMGRALLDLLKDDARFELAVALAA--SSR----LGEPVYAGEDGLRFTREWPAA-- 62 699*****************************94..444....588899999999888888866.. PP TIGR00036 68 laekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfai 133 +++v iDf+ p + ++ + ++ + lV GTTG++++ +++l ++a + ++l+ a+Nf++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 63 ----APEVAIDFSGPAGLGAALAHCRAHRIALVTGTTGLDQALQQQLDEAARD--IPLLRAANFSL 122 ....9************************************************..*********** PP TIGR00036 134 GvnlllkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveereglt 199 Gv +l +l+++aa l d+D++i+E+HH+ K+DaPSGTAl+l+e+ a+ rg l + av+ reg t lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 123 GVAVLRRLVRQAAAALPDWDLDILEAHHNRKVDAPSGTALALGEAAAAGRGVSLADGAVYAREGTT 188 ****************************************************************** PP TIGR00036 200 GerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydl 265 G r++ +iG+a vRggd+vgeh+v+ + Ger+e++H+a++R++fa+G+++a++wl+ + + ydl lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 189 GPRQHGSIGFAVVRGGDIVGEHEVWVIGPGERVELNHRATDRSIFARGAIEAAHWLAGRAPGAYDL 254 ****************************************************************** PP TIGR00036 266 edvl 269 + +l lcl|FitnessBrowser__Dyella79:N515DRAFT_2721 255 DAML 258 9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (266 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: 9.47 // [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