Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolinate reductase
Query= BRENDA::Q3MFY8 (278 letters) >FitnessBrowser__SynE:Synpcc7942_2136 Length = 273 Score = 387 bits (995), Expect = e-112 Identities = 193/273 (70%), Positives = 229/273 (83%), Gaps = 3/273 (1%) Query: 6 PIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPITN 65 PIPV+VNGA GKMGRE +KAIA A D+ L+GAI S + QG+D GE+ GL PLEVP+TN Sbjct: 4 PIPVVVNGATGKMGRETIKAIAAADDVTLVGAIARSADVQGQDIGEIVGLG-PLEVPVTN 62 Query: 66 QLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNLAD 125 LE ML + ER+ P V+VDFTHPD +YDNVR AIAYG+RPVVGTTGL+ Q+Q LA+ Sbjct: 63 DLEGMLCLASQEREVP--VVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAE 120 Query: 126 FAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTAEL 185 FAEKAS GCL+IPNFSIGMVLL QAA+ AS+++DHVEI+ELHH+QKADAPSGTAI+TA++ Sbjct: 121 FAEKASVGCLVIPNFSIGMVLLMQAAIQASRFYDHVEILELHHDQKADAPSGTAIKTAQM 180 Query: 186 LAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTLRH 245 LAELGKTFN V E E +PGARG++ E IRIHSVRLPGLIAH+EVIFGAPG+I TLRH Sbjct: 181 LAELGKTFNPPKVTEKETMPGARGAVGPENIRIHSVRLPGLIAHEEVIFGAPGEILTLRH 240 Query: 246 DTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278 DT DR+CYMPGVLLA+RKV QL L+YGL++IL Sbjct: 241 DTMDRSCYMPGVLLAVRKVRQLTGLIYGLDRIL 273 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: 314 Number of extensions: 10 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: 273 Length adjustment: 25 Effective length of query: 253 Effective length of database: 248 Effective search space: 62744 Effective search space used: 62744 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 Synpcc7942_2136 Synpcc7942_2136 (dihydrodipicolinate 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.32083.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-93 299.1 0.0 1.8e-93 299.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.0 0.0 1.8e-93 1.8e-93 2 269 .. 5 273 .] 4 273 .] 0.96 Alignments for each domain: == domain 1 score: 299.0 bits; conditional E-value: 1.8e-93 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla. 69 i+v+v+Ga+G+mGre ika+++a+d+ lv+a+ ++ + qg+DiGe++g+g+++vpv++dle + la lcl|FitnessBrowser__SynE:Synpcc7942_2136 5 IPVVVNGATGKMGRETIKAIAAADDVTLVGAIA-RSADVQGQDIGEIVGLGPLEVPVTNDLEGMLCLAs 72 79*******************************.599**************************999988 PP TIGR00036 70 .ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnl 137 e+++ v++Dft+p+ ++nv+ a+++gvr+VvGTTG+++e+l+el+++aek++v++++ pNf+iG++l lcl|FitnessBrowser__SynE:Synpcc7942_2136 73 qEREVPVVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAEFAEKASVGCLVIPNFSIGMVL 141 8889999************************************************************** PP TIGR00036 138 llkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkk.. 204 l++++ +a++ ++v Ei+ElHH++K+DaPSGTA+k+a+++a+ + +++ v+e+e+++G+r++ lcl|FitnessBrowser__SynE:Synpcc7942_2136 142 LMQAAIQASRFYDHV--EILELHHDQKADAPSGTAIKTAQMLAELGK-TFNPPKVTEKETMPGARGAvg 207 *******99988888..***************************999.9****************7522 PP TIGR00036 205 .eeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269 e+i i++vR+++++++++v+F+ Ge l+++H++++R++++ Gv++a+r++ ++ ++y+l+ +l lcl|FitnessBrowser__SynE:Synpcc7942_2136 208 pENIRIHSVRLPGLIAHEEVIFGAPGEILTLRHDTMDRSCYMPGVLLAVRKVRQLTGLIYGLDRIL 273 26777*********************************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (273 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.56 // [ok]
This GapMind analysis is from Apr 09 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