Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate PP_4547 PP_4547 putative Glutamine synthetase
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Putida:PP_4547 Length = 454 Score = 176 bits (445), Expect = 2e-48 Identities = 134/380 (35%), Positives = 181/380 (47%), Gaps = 17/380 (4%) Query: 80 WDTGYGDMVMTPDLSTLRLIPW--LPGTALVIADLVWADGSEVAVS-PRSILRRQLDRLK 136 WD G D P +L +PW +P TA V + ++G +++ PR +L R ++ LK Sbjct: 74 WDVGDIDCRAYPLDGSLVRLPWRRVP-TAAVQVSMHPSEGLPASIADPRHVLLRTIEALK 132 Query: 137 ARGLVADVATELEFIVFDQPY----RQAWASGYRGLTPASDYNIDYAILASSRMEPLLRD 192 A G +A ELEF + DQ R A G P S Y + ++EP L D Sbjct: 133 ADGYHPVMACELEFYLLDQQRDAQGRPQPALDNDGGRPRSTQV--YGLRELEQIEPFLAD 190 Query: 193 IRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTF 252 + G+ E GQ EI + +AL D YK K +A HG F Sbjct: 191 LYAACKAQGIPARTAISEYAPGQVEITLEHGDALQAMDQAVRYKRLVKGVAHAHGMQACF 250 Query: 253 MAK-YDEREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYA 311 MAK + + G H+H+SL + G+ +FA + + + R VAG L LR+ L + Sbjct: 251 MAKPFAQLAGTGMHMHLSLADSAGNNLFASED--KAGTPLLRQAVAGMLRHLRDSLLLFC 308 Query: 312 PTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQNIR-VECRVPGGDVNQYLAVAAL 370 P NS++RF +S+AP A WG+DNRT +LRV G N R VE R+ G D N YLA AA+ Sbjct: 309 PNANSFRRFQANSYAPLAPTWGVDNRTVSLRVPGGPANSRHVEHRICGADANPYLAAAAI 368 Query: 371 IAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHY 430 +A +GI L P GN Y A E LP A + S REA GED + Y Sbjct: 369 LAASHWGIREQLDPGAPVEGNGYAQA-TEHLPTDWLTALDALQHSDWAREALGEDFLGVY 427 Query: 431 LNNARVELAAFNAAVT--DW 448 L R E F A V+ DW Sbjct: 428 LKVKRAEYRQFMAEVSEQDW 447 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: 531 Number of extensions: 38 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: 457 Length of database: 454 Length adjustment: 33 Effective length of query: 424 Effective length of database: 421 Effective search space: 178504 Effective search space used: 178504 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