Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 15417 b1297 putative glutamine synthetase (EC 6.3.1.2) (VIMSS)
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Keio:15417 Length = 472 Score = 163 bits (413), Expect = 1e-44 Identities = 133/440 (30%), Positives = 202/440 (45%), Gaps = 31/440 (7%) Query: 26 VIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAMASWDTGYG 85 V V TD+ G GKRI +G + + A+D+ N V + G G Sbjct: 40 VDVLLTDLNGCFRGKRIPVSSLKK--LEKGCYFPASVFAMDILGNVVE-------EAGLG 90 Query: 86 DMVMTPDLSTLRLIPWLPGTAL-------VIADLVWADGSEVAVSPRSILRRQLDRLKAR 138 + PD + + ++ L +A ++ +V DG+ V PR++L R +L+ R Sbjct: 91 QEMGEPDRTCVPVLGSLTPSAADPEFIGQMLLTMVDEDGAPFDVEPRNVLNRLWQQLRQR 150 Query: 139 GLVADVATELEFIVFDQPYRQAWASGYR------GLTPASDYNIDYAILASSRMEPLLRD 192 GL VA ELEF + D RQ A GY G + + Y++ + +L D Sbjct: 151 GLFPVVAVELEFYLLD---RQRDAEGYLQPPCAPGTDDRNTQSQVYSVDNLNHFADVLND 207 Query: 193 IRLGMAGAGLRFEAVKGECNMGQQEIG-FRYDEALVTCDNHAIYKNGAKEIADQHGKSLT 251 I + + E + GQ EI + D L CD+ K + +A++H T Sbjct: 208 IDELAQLQLIPADGAVAEASPGQFEINLYHTDNVLEACDDALALKRLVRLMAEKHKMHAT 267 Query: 252 FMAK-YDEREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCY 310 FMAK Y+E G+ HIH+S++ G V +D+ G S + + +AG + + Sbjct: 268 FMAKPYEEHAGSGMHIHISMQNNRGENVLSDAEGED--SPLLKKMLAGMIDLMPSSMALL 325 Query: 311 APTINSYKRFADSSFAPTALAWGLDNRTCALRV-VGHGQNIRVECRVPGGDVNQYLAVAA 369 AP +NSY+RF + PT +WG +NRT ALR+ G N RVE RV G D N YL +AA Sbjct: 326 APNVNSYRRFQPGMYVPTQASWGHNNRTVALRIPCGDRHNHRVEYRVAGADANPYLVMAA 385 Query: 370 LIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAH 429 + AG L+G++ L L E GN + + P+ +DA F ++ +R GE Sbjct: 386 IFAGILHGLDNELPLQEEVEGNGLEQEGLP-FPIRQSDALGEFIENDHLRRYLGERFCHV 444 Query: 430 YLNNARVELAAFNAAVTDWE 449 Y EL F +T+ E Sbjct: 445 YHACKNDELLQFERLITETE 464 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: 520 Number of extensions: 27 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: 457 Length of database: 472 Length adjustment: 33 Effective length of query: 424 Effective length of database: 439 Effective search space: 186136 Effective search space used: 186136 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 09 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