Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate WP_010531457.1 ON01_RS12820 4-hydroxy-tetrahydrodipicolinate synthase
Query= metacyc::MONOMER-6565 (289 letters) >NCBI__GCF_000224785.1:WP_010531457.1 Length = 295 Score = 368 bits (945), Expect = e-107 Identities = 175/286 (61%), Positives = 234/286 (81%) Query: 1 MNFGNIATAMVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVAL 60 MNFG + TAMVTPFD+N +IDF L++YL+ NG+D LVVAGTTGESPTL+ EK+ L Sbjct: 1 MNFGQVLTAMVTPFDQNGDIDFNATRTLVNYLIANGSDGLVVAGTTGESPTLTNNEKLDL 60 Query: 61 IQYSVKEAAGRAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHF 120 ++ + A GRA +IAGTGSN+T ASI+LT++AE G DA+ML TPYYNKPSQEG+Y+H+ Sbjct: 61 FRFVAQVADGRAAVIAGTGSNSTWASIELTQQAEATGIDAIMLTTPYYNKPSQEGLYQHY 120 Query: 121 RAIAEETSLPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPE 180 +AIA+ TSLPVMLYNVPGR+A ++APETTIRL+EI NI+++KEASG+LDA+T+IV++T + Sbjct: 121 KAIAQATSLPVMLYNVPGRSAVAIAPETTIRLSEISNIVSVKEASGNLDAMTEIVSKTSD 180 Query: 181 DFAVYSGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPL 240 +F +YSGDDSLTLPAL++G G++SVASHIIG +M+EM + + G+ AA IHQKLLP Sbjct: 181 EFTLYSGDDSLTLPALTIGGSGVISVASHIIGSDMKEMAQSFKNGDVQNAAFIHQKLLPT 240 Query: 241 MKGLFAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSLM 286 M+ LFA P+PSP+K AL + G+ VG VRLP+IPL+ +E+ +L ++ Sbjct: 241 MQALFAQPSPSPVKAALNMMGIYVGDVRLPMIPLSSEEKQQLRQML 286 Lambda K H 0.313 0.131 0.357 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: 315 Number of extensions: 8 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: 289 Length of database: 295 Length adjustment: 26 Effective length of query: 263 Effective length of database: 269 Effective search space: 70747 Effective search space used: 70747 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_010531457.1 ON01_RS12820 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.3921554.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-115 369.9 0.2 3.8e-115 369.6 0.2 1.0 1 NCBI__GCF_000224785.1:WP_010531457.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010531457.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.6 0.2 3.8e-115 3.8e-115 2 283 .. 6 286 .. 5 288 .. 0.99 Alignments for each domain: == domain 1 score: 369.6 bits; conditional E-value: 3.8e-115 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 vltA++TPf+++g++df+a +l++++i++g+d++vv+GtTGEs+tL+ +Ek ++++++++++++r viaGt NCBI__GCF_000224785.1:WP_010531457.1 6 VLTAMVTPFDQNGDIDFNATRTLVNYLIANGSDGLVVAGTTGESPTLTNNEKLDLFRFVAQVADGRAAVIAGT 78 89*********************************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147 gsn+t +ielt++ae +g+d+++++tPyYnkP+qeGly+h+kaia++++lP++lYnvP+R++v ++pet++r NCBI__GCF_000224785.1:WP_010531457.1 79 GSNSTWASIELTQQAEATGIDAIMLTTPYYNKPSQEGLYQHYKAIAQATSLPVMLYNVPGRSAVAIAPETTIR 151 ************************************************************************* PP TIGR00674 148 LaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaale 220 L+e +iv++Keasg+l+ ++ei+++++++f+++sGdD+ltl+ l++G++GviSVas+++++++kem + + + NCBI__GCF_000224785.1:WP_010531457.1 152 LSEISNIVSVKEASGNLDAMTEIVSKTSDEFTLYSGDDSLTLPALTIGGSGVISVASHIIGSDMKEMAQSFKN 224 ************************************************************************* PP TIGR00674 221 gdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevl 283 gd+++a+ ihqkll++++alf ++ P pvK+al+++g+ ++ ++RlP+ +ls+e+k++l+++l NCBI__GCF_000224785.1:WP_010531457.1 225 GDVQNAAFIHQKLLPTMQALFAQPSPSPVKAALNMMGIYVG-DVRLPMIPLSSEEKQQLRQML 286 *****************************************.9****************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (295 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 21.31 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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