Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_012050080.1 SWIT_RS19690 glutamate 5-kinase
Query= reanno::Korea:Ga0059261_3512 (367 letters) >NCBI__GCF_000016765.1:WP_012050080.1 Length = 380 Score = 495 bits (1274), Expect = e-145 Identities = 270/369 (73%), Positives = 297/369 (80%), Gaps = 5/369 (1%) Query: 4 FPPASCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGAR 63 F PA+CPRLVVKIGSALLVDP+G +RRDWL+G+ ADIA R RAGQ+IAVVSSGAIALGAR Sbjct: 12 FTPAACPRLVVKIGSALLVDPDGRVRRDWLQGVVADIAERHRAGQRIAVVSSGAIALGAR 71 Query: 64 RLKLAKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNA 123 RL L KGGRASLEDAQAAAATGQIALS WAE+L A GLTAAQ+LVTLDDLEDRRRYLNA Sbjct: 72 RLALPKGGRASLEDAQAAAATGQIALSHCWAELLHAEGLTAAQILVTLDDLEDRRRYLNA 131 Query: 124 AATLGRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDR 183 A+TL RLL LGVVPVINENDSVATAEIRFGDNDRLAAR+ QAADA GV+LLSDIDGLY Sbjct: 132 ASTLHRLLGLGVVPVINENDSVATAEIRFGDNDRLAARIGQAADAGGVILLSDIDGLYTA 191 Query: 184 NPAL-PGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANG 242 NP P A +P V RID R+ MAD SASGMGSGGM+SK+EAARIA +G LAI G Sbjct: 192 NPHRDPTARLVPEVARIDARIRAMADADSASGMGSGGMISKLEAARIAQRSGAHLAIITG 251 Query: 243 RVDRPLS---ADARHTVFLPEKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAI 299 + D PL+ AD R TVFL EK ARKAWLAGRLTAKG I+VDAGA AL +GRSLLA Sbjct: 252 KRDHPLAAFDADHRGTVFLGEKIGTARKAWLAGRLTAKGRIVVDAGAVGALAQGRSLLAA 311 Query: 300 GATAIRGMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTL 358 GA + G F RGD+V I P+G IARGL EYDA DA I+G RS+ +ILGYAPRS L Sbjct: 312 GAVRVEGRFARGDVVDIVAPDGQAIARGLIEYDAVDAAKIVGRRSNAHEQILGYAPRSAL 371 Query: 359 VHRNHMALL 367 VHR+HM LL Sbjct: 372 VHRDHMVLL 380 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: 470 Number of extensions: 12 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: 367 Length of database: 380 Length adjustment: 30 Effective length of query: 337 Effective length of database: 350 Effective search space: 117950 Effective search space used: 117950 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: 50 (23.9 bits)
Align candidate WP_012050080.1 SWIT_RS19690 (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.1958720.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-114 368.2 0.3 2.7e-114 368.0 0.3 1.0 1 NCBI__GCF_000016765.1:WP_012050080.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016765.1:WP_012050080.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.0 0.3 2.7e-114 2.7e-114 2 362 .. 19 378 .. 18 379 .. 0.96 Alignments for each domain: == domain 1 score: 368.0 bits; conditional E-value: 2.7e-114 TIGR01027 2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglper.pkklaekQalaa 73 r+VvK+Gs++L++++g+++r l+ +v+++a++++aG+++ +vsSGa+a G+++L lp+ ++l++ Qa+aa NCBI__GCF_000016765.1:WP_012050080.1 19 RLVVKIGSALLVDPDGRVRRDWLQGVVADIAERHRAGQRIAVVSSGAIALGARRLALPKGgRASLEDAQAAAA 91 79*******************************************************9972568********* PP TIGR01027 74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146 GQ +L + + +l++ gl+ aQiL t +dl++r+rylNa +tl++ll lgvvp++NEND+va++ei+fGDND NCBI__GCF_000016765.1:WP_012050080.1 92 TGQIALSHCWAELLHAEGLTAAQILVTLDDLEDRRRYLNAASTLHRLLGLGVVPVINENDSVATAEIRFGDND 164 ************************************************************************* PP TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkava.gssgssvGTGGmrtKleaae 218 +L+a + + +A +ll+d+dgLy+a+p+++p+A+l++ev +i++ ++a+a ++s+s +G GGm +Kleaa+ NCBI__GCF_000016765.1:WP_012050080.1 165 RLAARIGQAADAGGVILLSDIDGLYTANPHRDPTARLVPEVARIDARIRAMAdADSASGMGSGGMISKLEAAR 237 ************************************************99983567888************** PP TIGR01027 219 lAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgks 291 +A+r+g + i++g++ + +a + + + gt+f +k +rk+w++ ++akG+i+vd+ga+ al + g+s NCBI__GCF_000016765.1:WP_012050080.1 238 IAQRSGAHLAIITGKRDHPLA-AFDADHRGTVFLGEKI-GTARKAWLAGRLTAKGRIVVDAGAVGALAQ-GRS 307 ***************966665.6677889*****9877.68999***********************98.*** PP TIGR01027 292 LlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362 Ll+ag v veg+F rg+vv+i+a++gq i++gl +y++ + +ki+g++s+ e++Lgy ++ vhrd++v NCBI__GCF_000016765.1:WP_012050080.1 308 LLAAGAVRVEGRFARGDVVDIVAPDGQAIARGLIEYDAVDAAKIVGRRSNAHEQILGYAPRSALVHRDHMV 378 *********************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (380 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: 17.81 // [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