Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate GFF1139 PGA1_c11540 gamma-glutamylputrescine synthetase PuuA
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Phaeo:GFF1139 Length = 448 Score = 178 bits (451), Expect = 4e-49 Identities = 133/424 (31%), Positives = 195/424 (45%), Gaps = 15/424 (3%) Query: 25 TVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAMASWDTGY 84 T+ +A D+ G++ GKR+ D +A L VD+ V + ++TG Sbjct: 17 TIRIAACDLNGQMRGKRMPVG-LADKLADGAARMPISTLNVDLWGRDVEDNPLV-FETGD 74 Query: 85 GDMVMTPDLSTLRLIPWLPG-TALVIADLVWADGSEVAVSPRSILRRQLDRLKARGLVAD 143 D VM P +PWL +ALV + W DG PR +L L R + RG Sbjct: 75 ADGVMLPTERGAVPMPWLANPSALVPMAMYWEDGRPFMGDPRHVLADVLARYQQRGWRVV 134 Query: 144 VATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILAS----SRMEPLLRDIRLGMAG 199 ATE+EF + D + A + P + +D + S + D+ G Sbjct: 135 AATEMEFSLLDD----SGAQPAPPIDPLTGRELDQQSVLSVAELDAFDAFFTDLYEGSDA 190 Query: 200 AGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAK-YDE 258 G+ ++ E +GQ EI + EA+ D+ ++K K +A +HG + TFMAK Y E Sbjct: 191 MGIPAQSAISEAGLGQFEINLNHQEAMRAADDAWLFKALVKGLARKHGFAATFMAKPYAE 250 Query: 259 REGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTINSYK 318 GN H+H S+ DG+ VF D G S + + VAG L + TL AP NSY Sbjct: 251 EAGNGMHVHFSVEDEDGNNVFND--GTERGSGLLMNAVAGCLTAMPASTLILAPHGNSYD 308 Query: 319 RFADSSFAPTALAWGLDNRTCALRVVGHGQNIR-VECRVPGGDVNQYLAVAALIAGGLYG 377 R + AP + AW +NRT A+R+ G R +E RV GGD+N YL +A ++ L G Sbjct: 309 RLVPGAHAPVSAAWAYENRTAAIRIPGGSPKARRIEHRVAGGDINPYLMLAVVLGAALAG 368 Query: 378 IERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHYLNNARVE 437 IE G P P GN Y+ + +L A LF+ L+ + V+ + + R E Sbjct: 369 IEDGATPPAPSEGNIYEIDGLPQLAPDWKAAIDLFDSDPLIARILPDRVIRNLVMMKRQE 428 Query: 438 LAAF 441 A F Sbjct: 429 QAGF 432 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: 581 Number of extensions: 33 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: 448 Length adjustment: 33 Effective length of query: 424 Effective length of database: 415 Effective search space: 175960 Effective search space used: 175960 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