Align glutamate 5-kinase; EC 2.7.2.11 (characterized)
to candidate WP_013136150.1 ARNIT_RS11755 glutamate 5-kinase
Query= CharProtDB::CH_121311 (251 letters) >NCBI__GCF_000092245.1:WP_013136150.1 Length = 254 Score = 246 bits (628), Expect = 3e-70 Identities = 128/253 (50%), Positives = 178/253 (70%), Gaps = 2/253 (0%) Query: 1 MKRIVVKVGSHVISEENTLSFERLKNLVAFLAKLM--EKYEVILVTSAAISAGHTKLDID 58 MKRIV+KVGS V+ E N L+ +RL NLV +AKL +KYE+ILV+S A++AG+ L++D Sbjct: 1 MKRIVIKVGSAVLREGNVLAVDRLNNLVDLIAKLKAEKKYEIILVSSGAVAAGNITLELD 60 Query: 59 RKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDMMI 118 R ++N+Q LAAIGQP L+ Y + + Q+LL DFDSRK +K+AK +++++ Sbjct: 61 RTKVLNRQALAAIGQPLLMKHYKKRFREHGFTCAQMLLVANDFDSRKRSKNAKGVMEILL 120 Query: 119 NLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDA 178 I+PI+NEND A EE++ GDND L A+A FFDAD+LVILSD+DG YD NP E +A Sbjct: 121 ENNIIPILNENDVIANEELLIGDNDQLGAHAAIFFDADMLVILSDVDGLYDCNPHENPEA 180 Query: 179 KRLEKITHIKEEWLQATIKTGSEHGTGGIVTKLKAAKFLLEHNKKMFLASGFDLSVAKTF 238 K + ++ +KE+ L+ SE TGGIVTKLKAA LL+++K M+L+SGFDL+ A F Sbjct: 181 KMRKIVSFLKEDELEMKYSPNSEFATGGIVTKLKAANLLLKNDKMMYLSSGFDLTNAYDF 240 Query: 239 LLEDKQIGGTLFE 251 LL++ GTLF+ Sbjct: 241 LLKEDHKSGTLFK 253 Lambda K H 0.319 0.136 0.373 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: 228 Number of extensions: 16 Number of successful extensions: 2 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: 251 Length of database: 254 Length adjustment: 24 Effective length of query: 227 Effective length of database: 230 Effective search space: 52210 Effective search space used: 52210 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_013136150.1 ARNIT_RS11755 (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.10095.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-71 226.3 0.2 3.6e-71 226.1 0.2 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013136150.1 ARNIT_RS11755 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013136150.1 ARNIT_RS11755 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.1 0.2 3.6e-71 3.6e-71 1 252 [. 2 253 .. 2 254 .] 0.94 Alignments for each domain: == domain 1 score: 226.1 bits; conditional E-value: 3.6e-71 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaG.hevvivsSGavaaGleaLglperpkklaek 68 kriV+K+Gs++L e++ l+ +l++lv +aklk++ e+++vsSGavaaG +L l + +k+ ++ lcl|NCBI__GCF_000092245.1:WP_013136150.1 2 KRIVIKVGSAVLREGNV-LAVDRLNNLVDLIAKLKAEKkYEIILVSSGAVAAGNITLELDR--TKVLNR 67 69**********99988.****************9865169**************999975..467789 PP TIGR01027 69 QalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvav 137 Qalaa+GQ Lmk+y+k f ++g + aQ+LL ++d+ +r+r +Na+ +e lle++++pi+NEND +a lcl|NCBI__GCF_000092245.1:WP_013136150.1 68 QALAAIGQPLLMKHYKKRFREHGFTCAQMLLVANDFDSRKRSKNAKGVMEILLENNIIPILNENDVIAN 136 ********************************************************************* PP TIGR01027 138 eeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvG 206 ee+ +GDND+L a a+ +Ad+Lv+l+dvdgLyd++p++np+Ak+ + v+ ++e+ +++ s s++ lcl|NCBI__GCF_000092245.1:WP_013136150.1 137 EELLIGDNDQLGAHAAIFFDADMLVILSDVDGLYDCNPHENPEAKMRKIVSFLKEDELEMKYSPNSEFA 205 *************************************************************999999** PP TIGR01027 207 TGGmrtKleaaelAsragveviiasgekpekiadll..edaavgtlfe 252 TGG+ tKl+aa+l + +++ sg + + d+l ed++ gtlf+ lcl|NCBI__GCF_000092245.1:WP_013136150.1 206 TGGIVTKLKAANLLLKNDKMMYLSSGFDLTNAYDFLlkEDHKSGTLFK 253 ***************999999999999998888876335778888886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (254 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: 00:00:00.01 # Mc/sec: 7.72 // [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