Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_038150959.1 B076_RS0107640 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000483485.1:WP_038150959.1 Length = 255 Score = 325 bits (833), Expect = 6e-94 Identities = 163/254 (64%), Positives = 199/254 (78%) Query: 17 MGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVKDDFDVF 76 MG+ LI A +EG+ + AA+ER SSL+G+DAGELAG GK GV + L++V D+FDV Sbjct: 1 MGKNLIAAVEQVEGLTVSAAIERPESSLIGADAGELAGIGKLGVAIVGDLESVVDEFDVL 60 Query: 77 IDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVM 136 IDFT P T+ +L C ++ K +VIGTTGFDE+G AI AA IA++FAANFSVGVN+ Sbjct: 61 IDFTTPATTVRNLDVCARNAKKIVIGTTGFDESGLAAIDQAAEKIAVIFAANFSVGVNLC 120 Query: 137 LKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREG 196 LKLL++AA+V+ D DIE+IE HHRHKVDAPSGTAL MGE +A L ++LK+CAVY REG Sbjct: 121 LKLLKQAAEVLNDGYDIEVIEGHHRHKVDAPSGTALRMGEVVADTLGRNLKECAVYGREG 180 Query: 197 HTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSG 256 TGER P TIGFATVRAGDIVG+HT +FA GER+EITHKASSRMTFA GA RS LW+ Sbjct: 181 ITGERDPNTIGFATVRAGDIVGDHTVLFATEGERVEITHKASSRMTFAKGAARSCLWIQD 240 Query: 257 KESGLFDMRDVLDL 270 K+ GLFDM+DVL+L Sbjct: 241 KKKGLFDMQDVLNL 254 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: 241 Number of extensions: 4 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: 273 Length of database: 255 Length adjustment: 25 Effective length of query: 248 Effective length of database: 230 Effective search space: 57040 Effective search space used: 57040 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 WP_038150959.1 B076_RS0107640 (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.19926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-102 329.2 2.9 1.2e-102 329.1 2.9 1.0 1 lcl|NCBI__GCF_000483485.1:WP_038150959.1 B076_RS0107640 4-hydroxy-tetrahy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_038150959.1 B076_RS0107640 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 329.1 2.9 1.2e-102 1.2e-102 13 269 .. 1 252 [. 1 253 [. 0.99 Alignments for each domain: == domain 1 score: 329.1 bits; conditional E-value: 1.2e-102 TIGR00036 13 mGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDftt 81 mG+++i av++ e+l ++aa+er++ss+ g D+Gelagigk+gv++ dle+v +++dvliDftt lcl|NCBI__GCF_000483485.1:WP_038150959.1 1 MGKNLIAAVEQVEGLTVSAAIERPESSLIGADAGELAGIGKLGVAIVGDLESV----VDEFDVLIDFTT 65 9**************************************************99....9*********** PP TIGR00036 82 peavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvle 150 p +++ n+ +++++ +++V+GTTGf+e +l+++ ++aek +a+++a+Nf++Gvnl lkll++aa+vl+ lcl|NCBI__GCF_000483485.1:WP_038150959.1 66 PATTVRNLDVCARNAKKIVIGTTGFDESGLAAIDQAAEK--IAVIFAANFSVGVNLCLKLLKQAAEVLN 132 ***************************************..**************************** PP TIGR00036 151 dv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvv 218 d DiE+iE HHrhK+DaPSGTAl+++e++a++ g++lke+av++reg+tGer ++iG+a+vR+gd+v lcl|NCBI__GCF_000483485.1:WP_038150959.1 133 DGyDIEVIEGHHRHKVDAPSGTALRMGEVVADTLGRNLKECAVYGREGITGERDPNTIGFATVRAGDIV 201 955****************************************************************** PP TIGR00036 219 gehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269 g+htvlFa++Ger+eitHkassR++fakG+ r+ w++dk+++++d++dvl lcl|NCBI__GCF_000483485.1:WP_038150959.1 202 GDHTVLFATEGERVEITHKASSRMTFAKGAARSCLWIQDKKKGLFDMQDVL 252 **************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (255 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.42 // [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