Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate YP_425246.1 Rru_A0154 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_000013085.1:YP_425246.1 Length = 265 Score = 268 bits (685), Expect = 9e-77 Identities = 139/266 (52%), Positives = 183/266 (68%), Gaps = 1/266 (0%) Query: 1 MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60 M + +VG GRMG+ L++ + + LVG IER GSP G D G + G T+G+ + DD Sbjct: 1 MKIGIVGCAGRMGRMLLKEVSASPETTLVGGIERPGSPATGTDLGLLIGSETIGIGVGDD 60 Query: 61 PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120 +FA + V+DFT+PAA+V A LAA+ ++GTTG + + AA+ +V Sbjct: 61 AAELFAASDTVIDFTTPAATVTHAALAARHGSALIVGTTGMGPDHVAALERAAQKVPVVF 120 Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180 + NMS+GV LL L ++ A L +D+DIEILEMHHR KVDAPSGTAL LG+AAA GR I Sbjct: 121 APNMSVGVTLLMALTERVAGLL-KDDYDIEILEMHHRFKVDAPSGTALGLGKAAAAGRGI 179 Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240 L + + RVRDG TGPRE G+IGFATLRGG V+GDH+VI A GER+ L+H A +R++FA Sbjct: 180 DLDEMATRVRDGLTGPREPGSIGFATLRGGDVVGDHTVIFAAEGERIELTHRASNRAVFA 239 Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGL 266 +GA++AALW + PGLYSM DVLGL Sbjct: 240 KGALRAALWTRDRAPGLYSMHDVLGL 265 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: 288 Number of extensions: 14 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: 265 Length adjustment: 25 Effective length of query: 243 Effective length of database: 240 Effective search space: 58320 Effective search space used: 58320 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 YP_425246.1 Rru_A0154 (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.21138.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-88 281.4 0.2 4.5e-88 281.3 0.2 1.0 1 lcl|NCBI__GCF_000013085.1:YP_425246.1 Rru_A0154 4-hydroxy-tetrahydrodi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_425246.1 Rru_A0154 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.3 0.2 4.5e-88 4.5e-88 2 270 .] 1 264 [. 1 264 [. 0.98 Alignments for each domain: == domain 1 score: 281.3 bits; conditional E-value: 4.5e-88 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekka 73 +k+++ G aGrmGr ++k+v ++++ lv+ +er+gs+ +g+D+G l+g +g+ v dd + lcl|NCBI__GCF_000013085.1:YP_425246.1 1 MKIGIVGCAGRMGRMLLKEVSASPETTLVGGIERPGSPATGTDLGLLIGSETIGIGVGDDAAEL----FAAS 68 89*******************************************************9998866....6789 PP TIGR00036 74 dvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllklleka 145 d +iDfttp a++ ++++a+++g l+vGTTG+ +++++l+ +a+k v++v+apN+++Gv ll+ l+e + lcl|NCBI__GCF_000013085.1:YP_425246.1 69 DTVIDFTTPAATVTHAALAARHGSALIVGTTGMGPDHVAALERAAQK--VPVVFAPNMSVGVTLLMALTERV 138 ***********************************************..*********************** PP TIGR00036 146 akvled.vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggd 216 a l+d +DiEi+E+HHr K+DaPSGTAl l+++ a+ rg dl+e a r+gltG r+ +iG+a++Rggd lcl|NCBI__GCF_000013085.1:YP_425246.1 139 AGLLKDdYDIEILEMHHRFKVDAPSGTALGLGKAAAAGRGIDLDEMATRVRDGLTGPREPGSIGFATLRGGD 210 ***98527**************************************************************** PP TIGR00036 217 vvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 vvg+htv+Fa +Ger+e+tH+as+Ra+fakG++ra+ w d + ++y ++dvl+ lcl|NCBI__GCF_000013085.1:YP_425246.1 211 VVGDHTVIFAAEGERIELTHRASNRAVFAKGALRAALWTRDRAPGLYSMHDVLG 264 ****************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (265 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: 6.19 // [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