Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_068174313.1 HTA01S_RS19030 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_001592305.1:WP_068174313.1 Length = 443 Score = 194 bits (493), Expect = 5e-54 Identities = 139/436 (31%), Positives = 209/436 (47%), Gaps = 14/436 (3%) Query: 28 VAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVD--LNTVPGYAMASWDTGYG 85 +A D G L G++++ +A+ G+ LA+D ++PG + D + Sbjct: 12 IAVADTNGLLRGQKVAASELPGILAS-GMGMSPAQLALDPTDVFLSMPGVTDGTGD--FH 68 Query: 86 DMVMTPDLSTLRLIPW-LPGT-ALVIADLVWADGSEVAVSPRSILRRQLDRLKARGLVAD 143 D +T D + R IPW +P L +A+ G A PRS+LRR LDR A + Sbjct: 69 DSALTVDTGSRREIPWEVPSDQGLYLAEF---SGDAQAFCPRSVLRRVLDRAAAMDVFPK 125 Query: 144 VATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLRDIRLGMAGAGLR 203 + ELEF +F++ A Y L A+ + ++ + + G++ Sbjct: 126 LGYELEFTLFNETAETLQAKQYDQLRTATAHASHDLVIYQAAQSEFYNGVADFCEPLGIQ 185 Query: 204 FEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAKYDER-EGN 262 + E G E ++A+ D + KN + A + G++++FM ++ E+ + Sbjct: 186 LAKMHEEIGGGFMEACIAANKAMAAADQAVLLKNFLRVFAMRRGQTISFMPRWSEQADSQ 245 Query: 263 SCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTINSYKRFAD 322 S HIH+SL G F D+ H MS FR F+AG L EF L +APT+NS++RFA+ Sbjct: 246 SSHIHISLLDGKGRPCFWDAEAEHHMSRRFRHFIAGVQRYLPEFMLIFAPTVNSWRRFAE 305 Query: 323 SSFAPTALAWGLDNRTCALRVVGHG-QNIRVECRVPGGDVNQYLAVAALIAGGLYGIERG 381 +FAP A WG++NRT LRVVGH +IRVE R+P D N YL AA IA GL GIE+ Sbjct: 306 GTFAPPAFTWGIENRTTCLRVVGHSPSSIRVENRLPCADANHYLTAAASIAAGLAGIEQK 365 Query: 382 LQLPEPCVGNAYQGADVERLPV--TLADAAVLFEDSALVREAFGEDVVAHYLNNARVELA 439 L+ P VGN Y + P+ + A SA ++ GE V + + Sbjct: 366 LEPSAPTVGNGYLSDARQGPPLQPNMLAAVHALRQSACAKDWLGERFVETFSATREAQCK 425 Query: 440 AFNAAVTDWERIRGFE 455 +F ER R FE Sbjct: 426 SFAGKSLIDERRRFFE 441 Lambda K H 0.321 0.137 0.417 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: 482 Number of extensions: 24 Number of successful extensions: 3 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: 457 Length of database: 443 Length adjustment: 33 Effective length of query: 424 Effective length of database: 410 Effective search space: 173840 Effective search space used: 173840 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 (21.9 bits) S2: 51 (24.3 bits)
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