Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_055435843.1 ASC41_RS06575 glutamine synthetase
Query= BRENDA::Q5LGP1 (729 letters) >NCBI__GCF_001418085.1:WP_055435843.1 Length = 728 Score = 873 bits (2255), Expect = 0.0 Identities = 426/730 (58%), Positives = 556/730 (76%), Gaps = 5/730 (0%) Query: 1 MSKMRFFALQELSNRKPLEITTPSNKLSDYYASHVFDRKKMQEYLPKEAYKAVVDATEKG 60 MS +RFFA++E NRKP+ IT + S+ + +V+D KKM++ L +A+ ++ +A EKG Sbjct: 1 MSTLRFFAIKETLNRKPVVITEEKRR-SEIFGQNVYDSKKMRQTLTSDAFVSLTNAIEKG 59 Query: 61 TPISREMADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGEVIERFSG 120 I R +AD IA+ MK WA S VTHYTHWFQPLT TAEKHD F E E+ IE+F G Sbjct: 60 GKIDRTIADQIASAMKDWALSKGVTHYTHWFQPLTGATAEKHDAFFETIENNGAIEKFGG 119 Query: 121 KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYK 180 L+QQEPDASSFPNGGIRNTFEARGYTAWD +SPAF+ TTLCIPT+F++YTGEALDYK Sbjct: 120 TQLVQQEPDASSFPNGGIRNTFEARGYTAWDPTSPAFIYGTTLCIPTVFVAYTGEALDYK 179 Query: 181 TPLLKALAAVDKAATEVCQLFDKNITRVFTNLGWEQEYFLVDTSLYNARPDLRLTGRTLM 240 TPLL+AL AVD AA VC+ FDKN+ +V +LGWEQEYFL+D++L ++RPD++LTGRTL+ Sbjct: 180 TPLLRALQAVDNAAVAVCKYFDKNVKKVNASLGWEQEYFLIDSALVSSRPDIQLTGRTLL 239 Query: 241 GHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIPVKTRHNEVAPNQFELAPIFEN 300 GH+SAK QQL+DHYFG+IP R ++M++LE EC LGIPVKTRHNEVAPNQFELAPI+E Sbjct: 240 GHASAKGQQLDDHYFGTIPNRAMSYMRDLETECMLLGIPVKTRHNEVAPNQFELAPIYEE 299 Query: 301 CNLANDHNQLVMDLMKRIARKHHFAVLFHEKPYNGVNGSGKHNNWSLCTDTGINLFAPGK 360 NLA DHN L+MD+M ++A +H+F VLFHEKP+ G+NGSGKHNNWSL TDTG+NL +PGK Sbjct: 300 ANLAVDHNALLMDVMDKVAERHNFKVLFHEKPFRGINGSGKHNNWSLSTDTGVNLLSPGK 359 Query: 361 NPKGNMLFLTFLVNVLMMVHKNQDLLRASIMSAGNSHRLGANEAPPAILSIFLGSQLSAT 420 P N+ FLTF +N + V+ N++LLRA+I SA N HRLGANEAPPAI+S+F+G QL+ Sbjct: 360 TPMSNLQFLTFFINTIKAVNDNEELLRAAIASASNDHRLGANEAPPAIISVFIGEQLTHV 419 Query: 421 LDEIVRQVTNSKMTPEEKTTLKLG-IGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSS 479 L+E+ VTN K++P+EKT LKL +G+IPEILLD TDRNRTSPFAFTGN+FEFRA GS Sbjct: 420 LNEL-ENVTNGKLSPQEKTDLKLNVVGKIPEILLDNTDRNRTSPFAFTGNKFEFRAVGSK 478 Query: 480 ANCAAAMIAINAAMANQLNEFKASVDKLM-EEGIGKDEAIFRILKENIIASEPIRFEGDG 538 ANCA M +N+ +A QL +FK VD L+ ++ + KDEA+F IL+E I S+ + FEG+G Sbjct: 479 ANCANPMTLLNSIVAKQLIDFKVEVDALIAKKDLKKDEAVFNILREYIKKSKAVLFEGNG 538 Query: 539 YSEEWKQEAARRGLTNICHVPEALMHYMDNQSRAVLIGERIFNETELACRLEVELEKYTM 598 Y E W++EA +RGL+N PEAL + ++ ++ + NETE+ R E+ELE Y M Sbjct: 539 YGEAWEKEAKKRGLSNNKSTPEALKVKVSKKALSLYKDLGVMNETEVVARYEIELEDYIM 598 Query: 599 KVQIESRVLGDLAINHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKEISH 658 ++QIE RVLGDLA NH+VP AV YQN L+EN+ +KEI+ E++++ +S + ELI+EIS Sbjct: 599 RIQIEGRVLGDLARNHVVPTAVKYQNILIENVKGLKEIY-EKDFKKVSKAQLELIEEISK 657 Query: 659 RVSAIKVLVRDMTEARKVANHKENFKEKAFAYEETVRPYLESIRDHIDHLEMEIDDEIWP 718 + +I LV +MT+ R+ +N ++ ++K+ Y V+P E IR H D LE+ +DDE+WP Sbjct: 658 HIESINKLVTNMTDIRRKSNLIKSLEDKSIVYCNKVKPLFEEIRYHCDKLELLVDDELWP 717 Query: 719 LPKYRELLFT 728 L KYRELLFT Sbjct: 718 LTKYRELLFT 727 Lambda K H 0.319 0.134 0.390 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: 1262 Number of extensions: 46 Number of successful extensions: 6 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: 729 Length of database: 728 Length adjustment: 40 Effective length of query: 689 Effective length of database: 688 Effective search space: 474032 Effective search space used: 474032 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: 55 (25.8 bits)
This GapMind analysis is from Jul 26 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