Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_012759697.1 RLEG_RS22035 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_000023185.1:WP_012759697.1 Length = 274 Score = 397 bits (1021), Expect = e-115 Identities = 204/268 (76%), Positives = 226/268 (84%) Query: 1 MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60 M LVVVGA GRMGQTLIR I SI+G L A+ER+GSPF+GKDAGE+ G+G GV + DD Sbjct: 6 MKLVVVGAAGRMGQTLIRLIHSIDGVTLHAAVERAGSPFVGKDAGEIAGLGPTGVIVGDD 65 Query: 61 PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120 PL F A GVLDFTSPAA+VEF+GLAAQARIVHVIGTTGC +D+ KI AAARHA IVK Sbjct: 66 PLNAFLDAEGVLDFTSPAATVEFSGLAAQARIVHVIGTTGCLPDDNAKIAAAARHARIVK 125 Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180 SGNMSLGVNLLSVL ++AA AL P+D+DIEILEMHH+HKVDAPSGTALL GEAAA+GR I Sbjct: 126 SGNMSLGVNLLSVLAEQAARALDPDDWDIEILEMHHKHKVDAPSGTALLFGEAAAKGRSI 185 Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240 LA SVRVRDG+TG RE G IGFATLRGGSVIG+HSV+ AG GE V LSH A DRSIFA Sbjct: 186 DLAAKSVRVRDGHTGAREAGTIGFATLRGGSVIGEHSVLFAGEGEIVTLSHSAADRSIFA 245 Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLNT 268 RGAIKAALWA KKPGLYSMLDVLGL++ Sbjct: 246 RGAIKAALWARDKKPGLYSMLDVLGLSS 273 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: 305 Number of extensions: 10 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: 268 Length of database: 274 Length adjustment: 25 Effective length of query: 243 Effective length of database: 249 Effective search space: 60507 Effective search space used: 60507 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_012759697.1 RLEG_RS22035 (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.1777.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-81 259.5 0.9 2.2e-81 259.3 0.9 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012759697.1 RLEG_RS22035 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012759697.1 RLEG_RS22035 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.3 0.9 2.2e-81 2.2e-81 2 270 .] 6 270 .. 5 270 .. 0.97 Alignments for each domain: == domain 1 score: 259.3 bits; conditional E-value: 2.2e-81 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 +k++v GaaGrmG+ +i+ +++ +++ l aa+er gs+ +gkD+Ge+ag+g++gv v dd + lcl|NCBI__GCF_000023185.1:WP_012759697.1 6 MKLVVVGAAGRMGQTLIRLIHSIDGVTLHAAVERAGSPFVGKDAGEIAGLGPTGVIVGDDPLNA----F 70 9******************************************************887775433....5 PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 +a+ ++Dft p a++e +a+++ + V+GTTG +d ++++++a + +++v + N+++Gvnll lcl|NCBI__GCF_000023185.1:WP_012759697.1 71 LDAEGVLDFTSPAATVEFSGLAAQARIVHVIGTTGCLPDDNAKIAAAARH--ARIVKSGNMSLGVNLLS 137 7888899*****************************************99..9**************** PP TIGR00036 140 kllekaakvle..dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkee 206 l+e+aa+ l+ d+DiEi+E+HH+hK+DaPSGTAl +e+ ak r dl ++ v r+g+tG+r++ + lcl|NCBI__GCF_000023185.1:WP_012759697.1 138 VLAEQAARALDpdDWDIEILEMHHKHKVDAPSGTALLFGEAAAKGRSIDLAAKSVRVRDGHTGAREAGT 206 **********55499****************************************************** PP TIGR00036 207 iGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 iG+a++Rgg v+geh+vlFa++Ge ++++H a +R++fa+G+++a+ w dk+ ++y + dvl+ lcl|NCBI__GCF_000023185.1:WP_012759697.1 207 IGFATLRGGSVIGEHSVLFAGEGEIVTLSHSAADRSIFARGAIKAALWARDKKPGLYSMLDVLG 270 **************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (274 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.08 // [ok]
This GapMind analysis is from Apr 10 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