Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate Echvi_4213 Echvi_4213 Glutamate 5-kinase
Query= curated2:Q1WRR5 (267 letters) >FitnessBrowser__Cola:Echvi_4213 Length = 263 Score = 135 bits (339), Expect = 1e-36 Identities = 88/265 (33%), Positives = 148/265 (55%), Gaps = 10/265 (3%) Query: 1 MENRNLQDAKRIVVKVGTSSLIRANGKINLQAIDELCYTLSGLVNEDKEVVLVSSGAVGV 60 MEN + + ++IVVKVG++ L +I + L L+ L ++ +L++SG+V Sbjct: 1 MENLS-KKPRKIVVKVGSNMLTNHKNRIMDTVLQHLVGQLAELYEDNIMPILITSGSVAA 59 Query: 61 GLANMGLVQRPKQ-IPEQQALAAIGQSQLMTIYQQRFAMYSQKTSQILLTHDVLTYPESR 119 G+ MG K +Q +++GQ +LM Y + F Y + Q+L T + + R Sbjct: 60 GMEAMGRELSIKDDAVRRQIYSSMGQPRLMRHYYEIFQQYGIRCGQVLATKRDFSPGKHR 119 Query: 120 ENVLNTFNELLKWKVIPVVNENDTVAVDEMDHQTSFGDNDWLSAVVASGIDADLLIVLSD 179 EN++N +N L+ ++P+ NE+DTV++ ++F DND L+A+VA ++AD+LI L+ Sbjct: 120 ENMINCYNGLIASGIVPIANEDDTVSLS----MSAFSDNDELAALVAELLEADMLIFLTH 175 Query: 180 IDGLFNKNPKKYADANLISEVTEINEKITGAAGGTG--SRFGTGGMATKIKAMDRMINEG 237 DG+FN P A ++ EV +I+EK G G G MA+K+K + ++ Sbjct: 176 KDGVFN-GPPDAAHTEVLEEV-KIDEKTEQYIHDKGDPKTIGRGNMASKLKMAKKAASKN 233 Query: 238 RKAVLANGKRPSIIFEILNGKQIGT 262 +ANG P+++ +I+NGKQIGT Sbjct: 234 IAVHIANGTTPNVLLDIVNGKQIGT 258 Lambda K H 0.315 0.133 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: 161 Number of extensions: 9 Number of successful extensions: 4 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: 267 Length of database: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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 Echvi_4213 Echvi_4213 (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.3688016.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-63 200.1 0.4 3.4e-63 199.9 0.4 1.0 1 FitnessBrowser__Cola:Echvi_4213 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Cola:Echvi_4213 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.9 0.4 3.4e-63 3.4e-63 2 253 .. 10 262 .. 9 263 .] 0.94 Alignments for each domain: == domain 1 score: 199.9 bits; conditional E-value: 3.4e-63 TIGR01027 2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpk.klaekQalaaVGQgr 78 +iVvK+Gs++Lt++++++ + l++lv q+a+l ++ ++++SG+vaaG+ea+g + k + +Q+ ++ GQ r FitnessBrowser__Cola:Echvi_4213 10 KIVVKVGSNMLTNHKNRIMDTVLQHLVGQLAELYEDNIMPILITSGSVAAGMEAMGRELSIKdDAVRRQIYSSMGQPR 87 8*******************************************************987655156789********** PP TIGR01027 79 LmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalv 156 Lm++y ++f+qyg++ +Q+L t++d+s ++ +N n + l++ g+vpi NE Dtv+ + f DND+L+alva l+ FitnessBrowser__Cola:Echvi_4213 88 LMRHYYEIFQQYGIRCGQVLATKRDFSPGKHRENMINCYNGLIASGIVPIANEDDTVSLSMSAFSDNDELAALVAELL 165 ****************************************************************************** PP TIGR01027 157 eAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagss.gssvGTGGmrtKleaaelAsragveviiasge 233 eAd+L+ lt dg+++ p ++ +++eev+ e++ ++++ ++ ++++G G m++Kl+ a+ A++ ++ v ia+g+ FitnessBrowser__Cola:Echvi_4213 166 EADMLIFLTHKDGVFNGPP-DAAHTEVLEEVKIDEKTEQYIHDKGdPKTIGRGNMASKLKMAKKAASKNIAVHIANGT 242 ****************999.78888999998877777777776665788***************************** PP TIGR01027 234 kpekiadlledaavgtlfea 253 +p+ ++d+++++++gt ++a FitnessBrowser__Cola:Echvi_4213 243 TPNVLLDIVNGKQIGTRVMA 262 ****************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (263 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: 10.74 // [ok]
This GapMind analysis is from Jul 25 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