Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_011338952.1 RSPH17029_RS17755 glutamate 5-kinase
Query= reanno::Korea:Ga0059261_3512 (367 letters) >NCBI__GCF_000015985.1:WP_011338952.1 Length = 370 Score = 308 bits (788), Expect = 2e-88 Identities = 187/365 (51%), Positives = 236/365 (64%), Gaps = 10/365 (2%) Query: 8 SCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKL 67 S RLVVKIGSALLVD EG +RR WL +A D+A G Q+ +VSSG+IALG R L L Sbjct: 10 SAKRLVVKIGSALLVDGEG-LRRQWLSALALDVAEARTRGTQVILVSSGSIALGRRVLHL 68 Query: 68 AKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATL 127 G A LE +QAAAA GQI L++ + EVLA +G+T AQ+LVTL+D EDRRRYLN+ AT+ Sbjct: 69 PPGPLA-LEQSQAAAAVGQIRLARAYEEVLAPHGITTAQVLVTLEDTEDRRRYLNSRATM 127 Query: 128 GRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNPAL 187 LL LG VP++NEND+VAT EIRFGDNDRLAA++A A +VLLSD+DG Y NP Sbjct: 128 ETLLGLGTVPIVNENDTVATDEIRFGDNDRLAAQIAVTVGADQLVLLSDVDGFYSANPKE 187 Query: 188 -PGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANGRVDR 246 P A +VE I +E MA SG+ GGM +KI AA+ A + G ++AI G R Sbjct: 188 DPTAERFDLVETITPALEAMAG-DPVSGLSKGGMKTKIMAAKTAVAGGCAMAITEGSAMR 246 Query: 247 PLSA---DARHTVFLPEKRTR-ARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIGAT 302 PL A A T F+ + + ARK W+ + +G+I VDAGA QAL G+SLL G Sbjct: 247 PLKALEQGAARTWFVAQGDPQAARKRWI-NAMKPRGTIRVDAGAVQALQAGKSLLPAGVV 305 Query: 303 AIRGMFFRGDLVTIEGPNGPI-ARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVHR 361 A+ G F RGD V I GP G + RGL+ Y A +A I G RS + ILGY+ R+ L+HR Sbjct: 306 AVEGNFGRGDPVEIAGPMGEVLGRGLTRYTAVEAVQIAGHRSAEIVAILGYSGRAALIHR 365 Query: 362 NHMAL 366 + M + Sbjct: 366 DDMVI 370 Lambda K H 0.319 0.134 0.377 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: 349 Number of extensions: 25 Number of successful extensions: 5 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: 367 Length of database: 370 Length adjustment: 30 Effective length of query: 337 Effective length of database: 340 Effective search space: 114580 Effective search space used: 114580 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: 49 (23.5 bits)
Align candidate WP_011338952.1 RSPH17029_RS17755 (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.30505.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-118 381.8 0.2 2e-118 381.6 0.2 1.0 1 lcl|NCBI__GCF_000015985.1:WP_011338952.1 RSPH17029_RS17755 glutamate 5-ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_011338952.1 RSPH17029_RS17755 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.6 0.2 2e-118 2e-118 1 363 [] 12 370 .] 12 370 .] 0.97 Alignments for each domain: == domain 1 score: 381.6 bits; conditional E-value: 2e-118 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 kr+VvK+Gs++L++++g l+r+ l++l+ +va+ ++ G++v++vsSG++a G + L lp p l++ Q lcl|NCBI__GCF_000015985.1:WP_011338952.1 12 KRLVVKIGSALLVDGEG-LRRQWLSALALDVAEARTRGTQVILVSSGSIALGRRVLHLPPGPLALEQSQ 79 69**************9.*************************************************** PP TIGR01027 70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138 a+aaVGQ rL ++ye++++ +g+++aQ+L t +d ++r+rylN r+t+e+ll lg vpivNENDtva++ lcl|NCBI__GCF_000015985.1:WP_011338952.1 80 AAAAVGQIRLARAYEEVLAPHGITTAQVLVTLEDTEDRRRYLNSRATMETLLGLGTVPIVNENDTVATD 148 ********************************************************************* PP TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207 ei+fGDND+L+a++a v+Ad+Lvll+dvdg y+a+p+++p+A++++ ve i+ +l+a+ag+ s + lcl|NCBI__GCF_000015985.1:WP_011338952.1 149 EIRFGDNDRLAAQIAVTVGADQLVLLSDVDGFYSANPKEDPTAERFDLVETITPALEAMAGDPVSGLSK 217 ********************************************************************* PP TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276 GGm+tK+ aa++A + g + i++g+ + ++le+ a t f a+ +rk+wi a++ ++G+i lcl|NCBI__GCF_000015985.1:WP_011338952.1 218 GGMKTKIMAAKTAVAGGCAMAITEGSAMRPL-KALEQGAARTWFVAQGDPQAARKRWINAMK-PRGTIR 284 **************************86665.667777889*****************8765.56**** PP TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345 vd+ga++al++ gksLlpagvv+vegnF rg+ vei + g+ +g+gl++y++ e +i+g++s+ei + lcl|NCBI__GCF_000015985.1:WP_011338952.1 285 VDAGAVQALQA-GKSLLPAGVVAVEGNFGRGDPVEIAGPMGEVLGRGLTRYTAVEAVQIAGHRSAEIVA 352 *********99.********************************************************* PP TIGR01027 346 vLgyekkeevvhrdnlvl 363 +Lgy+ ++ +hrd++v+ lcl|NCBI__GCF_000015985.1:WP_011338952.1 353 ILGYSGRAALIHRDDMVI 370 ****************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (370 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: 10.64 // [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