Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate PP_5299 PP_5299 glutamate-putrescine ligase
Query= curated2:P36205 (439 letters) >FitnessBrowser__Putida:PP_5299 Length = 460 Score = 191 bits (485), Expect = 4e-53 Identities = 139/448 (31%), Positives = 224/448 (50%), Gaps = 35/448 (7%) Query: 14 NVRFIRLQFTDINGTLKNLEITPDVFLESWEDGIMF---------DGSSIEGF---VRIE 61 + +++ L +D+NG ++ I + +E GI +GS++E + I Sbjct: 23 DTQYVDLLISDMNGVVRGKRIERASLHKVYEKGINLPASLFALDINGSTVESTGLGLDIG 82 Query: 62 ESDMYLKPVLDTFAVLPWTVDGAKSARVICDVYTPDGKPFEGDPRYRLRRMMEKAEQLGY 121 ++D P+ T + PW +A+++ ++ DG+PF DPR LR+++ K + LG Sbjct: 83 DADRICFPIPGTLSDEPW--QKRPTAQLLMTMHELDGQPFFADPREVLRQVVSKFDDLGL 140 Query: 122 TPYAGPEMEFFILPI-NEKGEPVPEFLDHGG-------YFDLLPLSKVEEIRRDIAIALE 173 T A E+EF+++ N G P P G + + L + + +D+ A + Sbjct: 141 TICAAFELEFYLIDQDNLNGRPQPPRSPISGKRPQSTQVYLIDDLDEYADCLQDMLEAAK 200 Query: 174 KMGITVEATHHEVAPSQHEVDFRYDTF-LRTADNAQTVKLVIKTMAIFHGYHATFMPKPF 232 + G+ +A E AP+Q EV+ + L+ D A +K +IK +A H TFM KP+ Sbjct: 201 EQGLPADAIVKESAPAQFEVNLHHVADPLKACDYAILLKRLIKNVAYDHEMDTTFMAKPY 260 Query: 233 YGVNGSGMHVHMSLF--RGDKNAFYDPDDPLGLSKELRYFVGGILKHAKALAAVTNPTIN 290 G G+G+HVH+SL + KN F DDPL S LR+ +GG+L+ A A P IN Sbjct: 261 PGQAGNGLHVHISLLDKKTGKNIFAS-DDPLQ-SDTLRHAIGGVLETMPASMAFLCPNIN 318 Query: 291 SYKRLVPGYEAPVYISWSVGNRSALIRIPKARGKATRLEYRSPDPSCNIYLAFAAILAAG 350 SY+R + P SW + NR+ +R+P + RLE+R N YL AAILA Sbjct: 319 SYRRFGAQFYVPNAPSWGLDNRTVAVRVPTDSSENVRLEHRVAGADANPYLMLAAILAGV 378 Query: 351 LDGIINKIEPPAPVEENIYHMTSERREELNIESLPGSLKEAVEELKKDDVIIDALGEHIF 410 G+ NK+EP AP+E N Y E+L +SLP +L++A+ L +V+ + Sbjct: 379 HHGLTNKVEPEAPIEGNSY-------EQLE-QSLPNNLRDALRALDDSEVLNQYISPDYI 430 Query: 411 EKFVEAAEKDWKEFSTYVTNWELQRYLY 438 + FV E + EF +++ E YL+ Sbjct: 431 DIFVACKESELAEFEVSISDLEYNWYLH 458 Lambda K H 0.320 0.139 0.414 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: 468 Number of extensions: 16 Number of successful extensions: 4 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: 439 Length of database: 460 Length adjustment: 33 Effective length of query: 406 Effective length of database: 427 Effective search space: 173362 Effective search space used: 173362 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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