Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate CA265_RS24865 CA265_RS24865 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Pedo557:CA265_RS24865 Length = 453 Score = 203 bits (516), Expect = 1e-56 Identities = 138/434 (31%), Positives = 196/434 (45%), Gaps = 5/434 (1%) Query: 26 VIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAMASWDTGYG 85 V +A D+ G L GK ++ F + R + C D W TGY Sbjct: 19 VKLAVADIDGILRGKYVAAEKFASLVEGR-LGFCDVTFGWDAGDVAYENGKYTGWHTGYP 77 Query: 86 DMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVSPRSILRRQLDRLKARGLVADVA 145 D + DL+T R IPW + D + AV PR +L++ + + G A Sbjct: 78 DAQVKIDLTTFRKIPWENEVPFFLGDFINDQDQPNAVCPRQLLKKVITECENEGFSPLFA 137 Query: 146 TELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLRDIRLGMAGAGLRFE 205 E E+ F + G+ L P S Y+IL S+ + D+ + + E Sbjct: 138 QEFEWFNFSETPESIHEKGFANLKPLSPGMFGYSILRSTYRNEFMSDLFDLLNKFDIPIE 197 Query: 206 AVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAKYDER-EGNSC 264 + E G E +Y AL D ++K KEIA +HG TFMAK E G S Sbjct: 198 GLHTETGPGVYEAAIKYAPALQAADQAILFKTAVKEIAYKHGILATFMAKISENLPGCSG 257 Query: 265 HIHVSLRGTDGSA-VFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTINSYKRFADS 323 H+H SL D +F D MS +S++AGQL L APTINSYKR + Sbjct: 258 HVHQSLWDADKKTNLFYDEKDAAQMSDTMKSYIAGQLHCLPYLLPMIAPTINSYKRLVEG 317 Query: 324 SFAPTALAWGLDNRTCALRVV-GHGQNIRVECRVPGGDVNQYLAVAALIAGGLYGIERGL 382 ++APT + WG+DNRT ALR + G + R+E R+ G D N YLA++A +A G++G++ L Sbjct: 318 AWAPTTVTWGIDNRTTALRALPGSKKASRLETRIVGSDTNPYLALSACLAAGMFGVKNKL 377 Query: 383 QLPEPCV-GNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHYLNNARVELAAF 441 +L + GN Y L L +A ++S L G+D V H+ E + Sbjct: 378 KLNQAATKGNGYTDLSNGVLSRNLFEATQKMKNSDLAATLLGKDFVDHFTMTREWECKQY 437 Query: 442 NAAVTDWERIRGFE 455 VTDWE R E Sbjct: 438 AKVVTDWELKRYLE 451 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: 515 Number of extensions: 19 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: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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