Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate CCNA_03664 CCNA_03664 dihydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >FitnessBrowser__Caulo:CCNA_03664 Length = 257 Score = 232 bits (591), Expect = 7e-66 Identities = 135/264 (51%), Positives = 167/264 (63%), Gaps = 17/264 (6%) Query: 3 LVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDPL 62 + + GA GRMG+ + + ++ A + ER G DAGE G+ + L Sbjct: 7 IAIAGANGRMGRAVAQALEGRSDAVVAARFERPG------DAGE-------GLVARETAL 53 Query: 63 PVFAKAHGVLDFTSPAASVEFAG-LAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121 A A V+DFT P ASV A AA VIG+TG S E ++I AAA IV+S Sbjct: 54 ---AAAEAVIDFTLPEASVALAEEAAANGGPALVIGSTGFSDEQLDRIDAAATKIVIVRS 110 Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181 GN SLGVN+L LV++AA AL +D+DIE+ E HH+ K+DAPSGTAL+LGEAAA GR I Sbjct: 111 GNYSLGVNMLMGLVRQAAAALPAQDWDIEVFEAHHKRKIDAPSGTALMLGEAAAEGRGIN 170 Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241 LA S R RDG TGPR+ G IGF+ +RGG +IG+HSVI AG E + LSH A DR +FAR Sbjct: 171 LAKVSDRGRDGVTGPRKDGDIGFSVVRGGGIIGEHSVIFAGESESLTLSHSAIDRGLFAR 230 Query: 242 GAIKAALWAHGKKPGLYSMLDVLG 265 GAI AA+W GK PGLY M DVLG Sbjct: 231 GAIAAAVWVKGKPPGLYDMQDVLG 254 Lambda K H 0.318 0.136 0.387 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: 230 Number of extensions: 13 Number of successful extensions: 3 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: 268 Length of database: 257 Length adjustment: 25 Effective length of query: 243 Effective length of database: 232 Effective search space: 56376 Effective search space used: 56376 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 CCNA_03664 CCNA_03664 (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.11626.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-70 221.4 0.7 3e-68 216.3 0.7 2.0 1 lcl|FitnessBrowser__Caulo:CCNA_03664 CCNA_03664 dihydrodipicolinate r Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03664 CCNA_03664 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.3 0.7 3e-68 3e-68 2 270 .] 5 254 .. 4 254 .. 0.92 Alignments for each domain: == domain 1 score: 216.3 bits; conditional E-value: 3e-68 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 +k+a+aGa GrmGr v +a++ d ++a +er D+Ge v e++l +a+ lcl|FitnessBrowser__Caulo:CCNA_03664 5 VKIAIAGANGRMGRAVAQALEGRSDAVVAARFER------PGDAGEGL----VAR--ETAL--------AAAE 57 69***********************999999996......34767622....222..2222........3568 PP TIGR00036 75 vliDfttpeavlenvkialek.gvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaa 146 +iDft+pea + ++ a+++ g lV+G TGfs+e+l ++ ++a k + +v + N+++Gvn+l+ l+++aa lcl|FitnessBrowser__Caulo:CCNA_03664 58 AVIDFTLPEASVALAEEAAANgGPALVIGSTGFSDEQLDRIDAAATK--IVIVRSGNYSLGVNMLMGLVRQAA 128 99***********998777662679**********************..***********************9 PP TIGR00036 147 kvl..edvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdv 217 l +d+DiE+ E+HH+ K DaPSGTAl l+e+ a+ rg +l ++ +r+g+tG rk+ +iG++ vRgg++ lcl|FitnessBrowser__Caulo:CCNA_03664 129 AALpaQDWDIEVFEAHHKRKIDAPSGTALMLGEAAAEGRGINLAKVSDRGRDGVTGPRKDGDIGFSVVRGGGI 201 99866899********************************99******************************* PP TIGR00036 218 vgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 +geh+v+Fa++ e l+++H a +R fa+G++ a+ w++ k ++yd++dvl+ lcl|FitnessBrowser__Caulo:CCNA_03664 202 IGEHSVIFAGESESLTLSHSAIDRGLFARGAIAAAVWVKGKPPGLYDMQDVLG 254 ***************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (257 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 1.90 // [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