Align Glutamate 5-kinase; LdG5K; Gamma-glutamyl kinase; EC 2.7.2.11 (characterized)
to candidate WP_011373042.1 SUDEN_RS07385 glutamate 5-kinase
Query= SwissProt::A0A0R6Y3I5 (263 letters) >NCBI__GCF_000012965.1:WP_011373042.1 Length = 254 Score = 237 bits (605), Expect = 2e-67 Identities = 123/250 (49%), Positives = 174/250 (69%) Query: 8 VKRIVVKVGSSILVDNQEIAAHRIEALCQFIADLQTKYEVILVTSGAVAAGYTKKEMDKS 67 +KR+VVKVGS++L +N IA R+ L F+ +L+ EVILV+SGAVAAGYT ++D+S Sbjct: 1 MKRVVVKVGSAVLTENDAIALQRMRNLVDFLVELRKSSEVILVSSGAVAAGYTALKLDRS 60 Query: 68 YVPNKQALASMGQPLLMHMYYTELQKHGILCAQMLLAAYDLDSRKRTINAHNTIEVLISH 127 + NKQALAS+GQP+LM Y + HGIL AQ+L+ A + + +T++ L+S+ Sbjct: 61 ILQNKQALASIGQPILMKKYAKKFATHGILTAQVLVTAANFKMEDESRKIKDTVDTLLSN 120 Query: 128 KVIPIINENDATALEELVFGDNDRLSALVAHHFKANLLVILSDIDGYYTENPRTSTNATI 187 VIPIINENDAT +ELV GDND+LSA VA + ++LL+ILSDID YY ++PR ++A Sbjct: 121 GVIPIINENDATTTKELVVGDNDQLSAYVAKYTDSDLLIILSDIDAYYDKDPRKFSDAKA 180 Query: 188 RSVVHELSPDDLVAEATPNNRFATGGIVTKLQAAQFLLERGGKMYLSSGFHLEKARQFLL 247 V+ + D+L +ATP+ FATGGI+TKL+AA +LL M L+SG++L+ + +L Sbjct: 181 LKTVNSVDADELEKDATPHGAFATGGILTKLKAANYLLNNKIDMVLTSGYNLDDIKSLML 240 Query: 248 GGSHEIGTLF 257 G+H GTLF Sbjct: 241 EGNHTGGTLF 250 Lambda K H 0.319 0.133 0.370 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: 209 Number of extensions: 7 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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_011373042.1 SUDEN_RS07385 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))
# 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/TIGR01027.hmm # target sequence database: /tmp/gapView.7404.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01027 [M=363] Accession: TIGR01027 Description: proB: glutamate 5-kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-71 225.6 4.7 5.7e-71 225.5 4.7 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373042.1 SUDEN_RS07385 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011373042.1 SUDEN_RS07385 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.5 4.7 5.7e-71 5.7e-71 1 252 [. 2 251 .. 2 254 .] 0.94 Alignments for each domain: == domain 1 score: 225.5 bits; conditional E-value: 5.7e-71 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 kr+VvK+Gs++Lte++ ++++++++lv + +l+k +ev++vsSGavaaG++aL l + l++kQ lcl|NCBI__GCF_000012965.1:WP_011373042.1 2 KRVVVKVGSAVLTENDA-IALQRMRNLVDFLVELRKS-SEVILVSSGAVAAGYTALKLDR--SILQNKQ 66 69***********9888.***************9875.89****************9986..5799*** PP TIGR01027 70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138 ala++GQ Lmk+y k+f+++g+ +aQ+L t+a++++++ + ++t+++ll++gv+pi+NEND+++++ lcl|NCBI__GCF_000012965.1:WP_011373042.1 67 ALASIGQPILMKKYAKKFATHGILTAQVLVTAANFKMEDESRKIKDTVDTLLSNGVIPIINENDATTTK 135 ********************************************************************* PP TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207 e+ +GDND+Lsa+va+ + dlL++l+d+d+ yd+dpr+ +dAk +++v++++++ + ++ ++ T lcl|NCBI__GCF_000012965.1:WP_011373042.1 136 ELVVGDNDQLSAYVAKYTDSDLLIILSDIDAYYDKDPRKFSDAKALKTVNSVDADELEKDATPHGAFAT 204 ****************************************************99999888888888*** PP TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlle.d.aavgtlfe 252 GG+ tKl+aa+ + ++++++sg + + i +l+ + ++ gtlf+ lcl|NCBI__GCF_000012965.1:WP_011373042.1 205 GGILTKLKAANYLLNNKIDMVLTSGYNLDDIKSLMLeGnHTGGTLFT 251 *****************************999876413134467765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (254 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: 00:00:00.00 # Mc/sec: 9.26 // [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