Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_085634936.1 MGEO_RS01580 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_002115805.1:WP_085634936.1 Length = 272 Score = 306 bits (785), Expect = 2e-88 Identities = 157/267 (58%), Positives = 193/267 (72%), Gaps = 1/267 (0%) Query: 1 MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60 +G+VV G GRMGQ L+ I L GA+ER+G ++GKD G G GV + DD Sbjct: 5 IGVVVTGVSGRMGQMLVSEIAKHPRMHLAGAVERAGHDWVGKDVGTAMGGAANGVIVADD 64 Query: 61 PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120 PL FA+A V+DFT+PAA+V FA LAAQAR VHVIGTTG S ED +I+ AARHA +V+ Sbjct: 65 PLDCFARAQAVIDFTAPAATVAFAELAAQARAVHVIGTTGLSDEDLTRIKTAARHAVVVR 124 Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180 +GNMSLGVNLL+VL +K A AL D+DIE++E HH KVDAPSGTAL+LGEAAA+GR + Sbjct: 125 AGNMSLGVNLLTVLTRKVAAALDA-DYDIEVIEYHHNKKVDAPSGTALMLGEAAAQGRGV 183 Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240 L + S R RDG TG R+ G IGF+ +RGG +IGDH V+ A GER+ L H A DR++FA Sbjct: 184 ELREVSDRGRDGITGARKRGDIGFSAIRGGDIIGDHDVLFAAEGERITLRHVASDRALFA 243 Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLN 267 RGA+KAALW K PG Y MLDVLGL+ Sbjct: 244 RGALKAALWGQDKAPGEYDMLDVLGLS 270 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: 264 Number of extensions: 10 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: 268 Length of database: 272 Length adjustment: 25 Effective length of query: 243 Effective length of database: 247 Effective search space: 60021 Effective search space used: 60021 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 WP_085634936.1 MGEO_RS01580 (4-hydroxy-tetrahydrodipicolinate 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.3816319.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-81 258.4 4.9 4.8e-81 258.2 4.9 1.0 1 NCBI__GCF_002115805.1:WP_085634936.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085634936.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.2 4.9 4.8e-81 4.8e-81 2 270 .] 5 268 .. 4 268 .. 0.96 Alignments for each domain: == domain 1 score: 258.2 bits; conditional E-value: 4.8e-81 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 i v+v+G +GrmG+ ++ ++++++ ++l++a+er g++ +gkD+G +g + gv v d ++ + +a+ NCBI__GCF_002115805.1:WP_085634936.1 5 IGVVVTGVSGRMGQMLVSEIAKHPRMHLAGAVERAGHDWVGKDVGTAMGGAANGVIVAD-DPLD---CFARAQ 73 679****************************************************5555.5556...678889 PP TIGR00036 75 vliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaak 147 +iDft p a++ +++a+++ V+GTTG+s+edl ++k +a + + +v a N+++Gvnll+ l++k+a NCBI__GCF_002115805.1:WP_085634936.1 74 AVIDFTAPAATVAFAELAAQARAVHVIGTTGLSDEDLTRIKTAARH--AVVVRAGNMSLGVNLLTVLTRKVAA 144 99*******************************************9..899******************9999 PP TIGR00036 148 vle.dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvg 219 l+ d+DiE+iE HH++K+DaPSGTAl l+e+ a+ rg +l+e+ +r+g+tG+rk+ +iG++a+Rggd++g NCBI__GCF_002115805.1:WP_085634936.1 145 ALDaDYDIEVIEYHHNKKVDAPSGTALMLGEAAAQGRGVELREVSDRGRDGITGARKRGDIGFSAIRGGDIIG 217 996599******************************************************************* PP TIGR00036 220 ehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 +h vlFa +Ger++++H as+Ra fa+G+++a+ w +dk+ + yd+ dvl+ NCBI__GCF_002115805.1:WP_085634936.1 218 DHDVLFAAEGERITLRHVASDRALFARGALKAALWGQDKAPGEYDMLDVLG 268 *************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (272 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: 16.62 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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