Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_005808837.1 DHAF_RS18285 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q3MFY8 (278 letters) >NCBI__GCF_000021925.1:WP_005808837.1 Length = 267 Score = 251 bits (641), Expect = 1e-71 Identities = 137/272 (50%), Positives = 177/272 (65%), Gaps = 9/272 (3%) Query: 7 IPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPITNQ 66 I V V+GA GKMGREVV+ I D+ L+GA D+ QG+D GEL ++ PL + IT Sbjct: 4 IRVFVSGAGGKMGREVVRTILDQEDMQLVGASDA--RQQGRDIGELLAMA-PLGIEITGP 60 Query: 67 LEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNLADF 126 LE VA ++ ++VDFT+P SV N + A+A G+ PV+GTTGL A I + D Sbjct: 61 LE-----VAHLKETRADIMVDFTNPQSVLKNAKCALAAGVVPVLGTTGLDEADISEIRDL 115 Query: 127 AEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTAELL 186 ++ G I PNF+IG +L+ + A A++YF HVEIIELHH+QK DAPSGTA++T E + Sbjct: 116 VDQTKVGAFIAPNFAIGAILMMRFAQEAAKYFPHVEIIELHHDQKLDAPSGTALKTVEWI 175 Query: 187 AELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTLRHD 246 +E+ K E EKI G+RG +GI IHSVRLPG IAHQEVIFG GQ T+RHD Sbjct: 176 SEVRKPLVQGHPNEYEKIKGSRGGDV-DGIHIHSVRLPGFIAHQEVIFGGLGQALTIRHD 234 Query: 247 TSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278 R YMPG++LA+RK QL +LV GLE L Sbjct: 235 ALSRETYMPGIMLAVRKASQLSNLVIGLENFL 266 Lambda K H 0.317 0.136 0.386 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: 210 Number of extensions: 8 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: 278 Length of database: 267 Length adjustment: 25 Effective length of query: 253 Effective length of database: 242 Effective search space: 61226 Effective search space used: 61226 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_005808837.1 DHAF_RS18285 (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.19184.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-91 290.2 0.3 9.5e-91 290.0 0.3 1.0 1 lcl|NCBI__GCF_000021925.1:WP_005808837.1 DHAF_RS18285 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_005808837.1 DHAF_RS18285 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.0 0.3 9.5e-91 9.5e-91 2 270 .] 4 267 .] 3 267 .] 0.98 Alignments for each domain: == domain 1 score: 290.0 bits; conditional E-value: 9.5e-91 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 i+v v+Ga+G+mGrev++++ ++ed++lv+a + +qg+DiGel ++++g++++ le + +l+e lcl|NCBI__GCF_000021925.1:WP_005808837.1 4 IRVFVSGAGGKMGREVVRTILDQEDMQLVGASD---ARQQGRDIGELLAMAPLGIEITGPLEVA-HLKE 68 99*******************************...599***********************77.**** PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 ++ad+++Dft p++vl+n+k+al++gv +V+GTTG++e+d++e++dl+++++v++ iapNfaiG++l++ lcl|NCBI__GCF_000021925.1:WP_005808837.1 69 TRADIMVDFTNPQSVLKNAKCALAAGVVPVLGTTGLDEADISEIRDLVDQTKVGAFIAPNFAIGAILMM 137 ********************************************************************* PP TIGR00036 140 kllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG 208 +++++aak++ +v EiiElHH++K DaPSGTAlk+ e i+++r+ l + + +e e ++G+r+ + G lcl|NCBI__GCF_000021925.1:WP_005808837.1 138 RFAQEAAKYFPHV--EIIELHHDQKLDAPSGTALKTVEWISEVRK-PLVQGHPNEYEKIKGSRGGDVDG 203 ************9..******************************.89*****************9999 PP TIGR00036 209 ..iaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 i++vR+++ +++++v+F++ G+ l+i+H+a sR++++ G+++a+r+ +++ ++v +le++l+ lcl|NCBI__GCF_000021925.1:WP_005808837.1 204 ihIHSVRLPGFIAHQEVIFGGLGQALTIRHDALSRETYMPGIMLAVRKASQLSNLVIGLENFLE 267 8899*********************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (267 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: 7.35 // [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