Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate WP_017549551.1 C792_RS0111235 glutamate 5-kinase
Query= curated2:B8DHP2 (276 letters) >NCBI__GCF_000330705.1:WP_017549551.1 Length = 277 Score = 279 bits (714), Expect = 4e-80 Identities = 136/269 (50%), Positives = 197/269 (73%) Query: 2 RESLKNSKRLVIKVGTSTLMYGNGHINLRTIEKLAMVLSDLRNEGKEVILVSSGAIGVGC 61 R+ LK KR+VIK+GT+++M ++ I++LA V S L+ +GKEV+LVSSGA+GVG Sbjct: 3 RDILKECKRVVIKIGTNSIMKSPTKVDYHKIDRLAFVCSSLQQQGKEVVLVSSGAVGVGA 62 Query: 62 HKLQLPVRPTSIPDLQAVASVGQSELMHIYSKFFGEYGQVVGQVLLTRDVTDFPISRENV 121 L++ P+++ + QA+ASVGQS LM++YS+FF Y Q VGQ+L+TRD+ ++P S N Sbjct: 63 STLKMDKYPSAVAEQQALASVGQSALMNLYSRFFQHYEQYVGQILMTRDIINYPNSYANC 122 Query: 122 MNTLDSLLSRGIIPIVNENDTVAVEELEHVTKYGDNDLLSAIVAKLVQADLLIMLSDIDG 181 +++SLL++ IIPI+NEND V+V+E H TK+G+ND L+A+VA+LV ADLLI++SD+DG Sbjct: 123 NTSINSLLNKDIIPIINENDAVSVDESGHCTKFGENDTLAAVVAELVDADLLIIMSDVDG 182 Query: 182 FYGSNPTTDPDAVMFSEINQITPEIEALAGGRGSKFGTGGMLTKLSAASYCMESNQKMIL 241 Y SNP T+P+A + S + +I +I ++AGG GS F TGGM TKL AA M N+ MI+ Sbjct: 183 LYDSNPHTNPEAELISYVGEIDTDILSMAGGAGSVFSTGGMETKLRAAQKMMSINKSMII 242 Query: 242 TNGKNPTVIFNIMQGEQVGTLFASKKEEL 270 T+ KNP +IF+I+ G+ GTLF + EL Sbjct: 243 TSAKNPNIIFDILNGQDAGTLFKKNEAEL 271 Lambda K H 0.316 0.134 0.369 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: 236 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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 WP_017549551.1 C792_RS0111235 (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.875077.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-90 289.1 1.8 3.2e-90 288.8 1.8 1.0 1 NCBI__GCF_000330705.1:WP_017549551.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549551.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.8 1.8 3.2e-90 3.2e-90 1 259 [. 10 272 .. 10 275 .. 0.98 Alignments for each domain: == domain 1 score: 288.8 bits; conditional E-value: 3.2e-90 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaa 73 kr+V+K+G++s++++ +k++ +k+ +l+ +++l+++G+evv+vsSGav +G+++L + + p +ae+Qala+ NCBI__GCF_000330705.1:WP_017549551.1 10 KRVVIKIGTNSIMKSPTKVDYHKIDRLAFVCSSLQQQGKEVVLVSSGAVGVGASTLKMDKYPSAVAEQQALAS 82 69*********************************************************************** PP TIGR01027 74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee....ikf 142 VGQ++Lm+ly++ f++y++ v+QiL+tr+ ++ + y N ++++++ll+ +++pi+NEND+v+v+e kf NCBI__GCF_000330705.1:WP_017549551.1 83 VGQSALMNLYSRFFQHYEQYVGQILMTRDIINYPNSYANCNTSINSLLNKDIIPIINENDAVSVDEsghcTKF 155 *****************************************************************9666669* PP TIGR01027 143 GDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKle 215 G+NDtL+a+va lv+AdlL++++dvdgLyd++p+tnp+A+li++v ei++++ ++ag++gs + TGGm+tKl NCBI__GCF_000330705.1:WP_017549551.1 156 GENDTLAAVVAELVDADLLIIMSDVDGLYDSNPHTNPEAELISYVGEIDTDILSMAGGAGSVFSTGGMETKLR 228 ************************************************************************* PP TIGR01027 216 aaelAsragveviiasgekpekiadlledaavgtlfeakkkklk 259 aa+ ++ + +ii+s+++p+ i d+l+++ gtlf++++++l+ NCBI__GCF_000330705.1:WP_017549551.1 229 AAQKMMSINKSMIITSAKNPNIIFDILNGQDAGTLFKKNEAELQ 272 **************************************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (277 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: 14.12 // [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