Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate WP_013430064.1 CALKRO_RS05445 glutamate 5-kinase
Query= curated2:Q8XHA6 (269 letters) >NCBI__GCF_000166775.1:WP_013430064.1 Length = 266 Score = 297 bits (761), Expect = 1e-85 Identities = 151/260 (58%), Positives = 200/260 (76%), Gaps = 4/260 (1%) Query: 7 DSKRIVVKVGTSTLTYENGSVNLMRIEKLSRVISDICNMGKEVVLVSSGAIGVGVGKLRL 66 ++K+IVVKVGTST+TY G +NL R+EKL+RV+SDI N G++VVLV+SGA+ G+G+L L Sbjct: 6 NAKKIVVKVGTSTVTYPTGKLNLSRLEKLARVLSDIKNEGRDVVLVTSGAVASGLGRLGL 65 Query: 67 EKKPETIREKQAVAAVGQCALMHIYNKFFGEYSHVVAQVLLTRDVLENERMKNNVCNTFD 126 K +T +EKQA+AA+GQ LM IY K FGEY VVAQVLLT+DV++ E+ NV NTF+ Sbjct: 66 TKNHKTTQEKQALAAIGQGILMQIYEKLFGEYGVVVAQVLLTKDVVDEEKKMLNVKNTFE 125 Query: 127 TLLEKGIIPIVNENDAISIDEIQNILNFGDNDNLSAIVSTLVNADTLIILSDIDGFYDSD 186 L + G IPIVNEND ++I+E L FGDND LSA V+T++ AD LIILSDIDG Y D Sbjct: 126 YLFKYGAIPIVNENDVVAIEE----LEFGDNDTLSAYVATIIGADLLIILSDIDGLYSCD 181 Query: 187 PRTNEDSKMLKEVYEITPEIEECAGGAGSNRGTGGMVTKLSAAKVATSNGIDMILANGEN 246 PR ++ ++++KEV+EI IE AGGAG+ TGGM TK+ AAK+A +GI M++ANGEN Sbjct: 182 PRIDKSAELIKEVFEIDSYIESIAGGAGTLNSTGGMQTKIEAAKIAMQHGIPMVIANGEN 241 Query: 247 PEILIDILNGEDIGTMFVAK 266 P I+ +IL G++IGT+FV+K Sbjct: 242 PSIVKEILEGKEIGTLFVSK 261 Lambda K H 0.315 0.134 0.366 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: 234 Number of extensions: 7 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: 269 Length of database: 266 Length adjustment: 25 Effective length of query: 244 Effective length of database: 241 Effective search space: 58804 Effective search space used: 58804 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: 42 (22.0 bits) S2: 47 (22.7 bits)
Align candidate WP_013430064.1 CALKRO_RS05445 (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.859179.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-98 314.5 3.2 5.6e-98 314.3 3.2 1.0 1 NCBI__GCF_000166775.1:WP_013430064.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430064.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.3 3.2 5.6e-98 5.6e-98 1 255 [. 8 262 .. 8 266 .] 0.99 Alignments for each domain: == domain 1 score: 314.3 bits; conditional E-value: 5.6e-98 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaa 73 k+iVvK+G+s++t ++gkl++s+l++l++ ++ +k++G++vv+v+SGava+Gl +Lgl++ k+ +ekQalaa NCBI__GCF_000166775.1:WP_013430064.1 8 KKIVVKVGTSTVTYPTGKLNLSRLEKLARVLSDIKNEGRDVVLVTSGAVASGLGRLGLTKNHKTTQEKQALAA 80 68*********************************************************************** PP TIGR01027 74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146 +GQg Lm+ yeklf +yg vaQ+LLt++ + ++++ lN +nt+e l++ g++pivNEND va+ee++fGDND NCBI__GCF_000166775.1:WP_013430064.1 81 IGQGILMQIYEKLFGEYGVVVAQVLLTKDVVDEEKKMLNVKNTFEYLFKYGAIPIVNENDVVAIEELEFGDND 153 ************************************************************************* PP TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaael 219 tLsa+va++++AdlL++l+d+dgLy++dpr + A+li+ev ei++ ++++ag++g+ + TGGm+tK+eaa++ NCBI__GCF_000166775.1:WP_013430064.1 154 TLSAYVATIIGADLLIILSDIDGLYSCDPRIDKSAELIKEVFEIDSYIESIAGGAGTLNSTGGMQTKIEAAKI 226 ************************************************************************* PP TIGR01027 220 Asragveviiasgekpekiadlledaavgtlfeakk 255 A++ g++++ia+ge+p+ + ++le++++gtlf +k+ NCBI__GCF_000166775.1:WP_013430064.1 227 AMQHGIPMVIANGENPSIVKEILEGKEIGTLFVSKN 262 ********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (266 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: 19.63 // [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