Align Glutamate 5-kinase 1; EC 2.7.2.11; Gamma-glutamyl kinase 1; GK 1 (uncharacterized)
to candidate 7026927 Shewana3_4056 gamma-glutamyl kinase (RefSeq)
Query= curated2:Q3IEY8 (368 letters) >FitnessBrowser__ANA3:7026927 Length = 368 Score = 470 bits (1209), Expect = e-137 Identities = 227/360 (63%), Positives = 290/360 (80%) Query: 7 RRIVLKVGSALIAPDQDGCRSRYILTIAQFIVRCRARGIEVILVSSGSVAAGAHLFPSDT 66 +RIV+KVGSALIAP + GC S Y+L IAQFI CR +GI+V+LVSSGSVAAG H F Sbjct: 7 KRIVVKVGSALIAPHKQGCSSHYLLGIAQFITYCRVQGIQVVLVSSGSVAAGWHHFEGQA 66 Query: 67 ARSVVMKKAMAAAGQTEMIAMWDRFFDFPSAQLLLTHGDLRDHERYQSIRETVFTLLEHG 126 SV +KKAMAAAGQ +M+A W++ FDFP+AQLLLTHGDLR+ ERY SIR+T+F+LLEHG Sbjct: 67 QPSVTVKKAMAAAGQADMMATWNKLFDFPTAQLLLTHGDLRNRERYISIRDTIFSLLEHG 126 Query: 127 VLPIINENDAVTTDDLKVGDNDNLSAMVAAAADADALLIFSDVDGLYDKNPNLHDDAILL 186 ++PIINENDAVT D LKVGDNDNLSAMVAAAADAD L+I SDVDGLYD+NP+ H +A L+ Sbjct: 127 LMPIINENDAVTADKLKVGDNDNLSAMVAAAADADTLVICSDVDGLYDQNPHEHPNAKLI 186 Query: 187 PEIKSIDDSIYAMAGCATSAVGTGGMKTKIEAAEKATSHGISTYIINGFKEETFTRLLAG 246 ++ I+ IYAMAG +S VGTGGM+TKI+AAEKA SHGI T+IINGF ++F++LL G Sbjct: 187 KQVTEINADIYAMAGGVSSDVGTGGMRTKIQAAEKAISHGIETFIINGFNADSFSQLLKG 246 Query: 247 ENPGTIFLPYEKPMQDSVHWMTHTANEQGEVVVDGSFDKSLEGETGCIRGDEIMAVHGEF 306 +NPGT+F PYEKPMQ+ +HWMTHT+ QGEV+V+ FD +L+ + + D+++ V G+F Sbjct: 247 QNPGTLFTPYEKPMQEHLHWMTHTSQAQGEVIVEDDFDLALDQHSEQLTSDDVVEVKGDF 306 Query: 307 AIGDTILVRSEDGTRLAKATANYSSCLLSFIADNEQSEFSEKMQDSIGPVISEKHIALLE 366 ++GDTILVR DGT+LAKA +NYSSCLLSFI + + F+ + Q GP+IS+K+IA+L+ Sbjct: 307 SVGDTILVRKGDGTKLAKAKSNYSSCLLSFITEQDDQAFASEFQQKTGPIISDKNIAILK 366 Lambda K H 0.318 0.133 0.382 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: 436 Number of extensions: 17 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate 7026927 Shewana3_4056 (gamma-glutamyl kinase (RefSeq))
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.20482.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-102 328.4 0.5 3.4e-102 328.2 0.5 1.0 1 lcl|FitnessBrowser__ANA3:7026927 Shewana3_4056 gamma-glutamyl kin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7026927 Shewana3_4056 gamma-glutamyl kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.2 0.5 3.4e-102 3.4e-102 1 350 [. 7 352 .. 7 364 .. 0.96 Alignments for each domain: == domain 1 score: 328.2 bits; conditional E-value: 3.4e-102 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQg 77 kriVvK+Gs++++ +++ ++++l +++ ++ + +G +vv+vsSG+vaaG+++ + +p +++ k a+aa GQ+ lcl|FitnessBrowser__ANA3:7026927 7 KRIVVKVGSALIAPHKQGCSSHYLLGIAQFITYCRVQGIQVVLVSSGSVAAGWHHFEGQAQP-SVTVKKAMAAAGQA 82 69******************************************************999888.58999********* PP TIGR01027 78 rLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaa 154 +m++++klf+ +aQ+LLt+ dl++rery r+t+ +lle g +pi+NEND+v+ +++k+GDND+Lsa+vaa lcl|FitnessBrowser__ANA3:7026927 83 DMMATWNKLFD---FPTAQLLLTHGDLRNRERYISIRDTIFSLLEHGLMPIINENDAVTADKLKVGDNDNLSAMVAA 156 ********997...589************************************************************ PP TIGR01027 155 lveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviias 231 +Ad+Lv+ +dvdgLyd++p+++p+Akli++v+ei++++ a+ag+ +s+vGTGGmrtK++aae A + g+e++i++ lcl|FitnessBrowser__ANA3:7026927 157 AADADTLVICSDVDGLYDQNPHEHPNAKLIKQVTEINADIYAMAGGVSSDVGTGGMRTKIQAAEKAISHGIETFIIN 233 ***********************************************9***************************** PP TIGR01027 232 gekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrge 308 g + ++ +ll++++ gtlf++ +k ++++ +w++++s+a+G++iv++ al ++ + L+ vvev+g+Fs g+ lcl|FitnessBrowser__ANA3:7026927 234 GFNADSFSQLLKGQNPGTLFTPYEKPMQEHLHWMTHTSQAQGEVIVEDDFDLALDQHSEQLTSDDVVEVKGDFSVGD 310 ***************************************************************************** PP TIGR01027 309 vveilaeegqeigkglvnysseelekikglkseeiedvLgye 350 ++ +++ +g++++k+++nyss l+ i+ + + + +++ + lcl|FitnessBrowser__ANA3:7026927 311 TILVRKGDGTKLAKAKSNYSSCLLSFITEQDDQAFASEFQQK 352 *************************99999998888877554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (368 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: 00:00:00.01 # Mc/sec: 12.28 // [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