Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf1N1B4_2254 Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Query= BRENDA::P36205 (439 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2254 Length = 426 Score = 186 bits (473), Expect = 9e-52 Identities = 130/435 (29%), Positives = 213/435 (48%), Gaps = 32/435 (7%) Query: 25 INGTLKNLEITPDVFLESWEDGIMF---------DGSSIEGF---VRIEESDMYLKPVLD 72 +NG ++ I + +E GI +GS++E + I ++D P+ D Sbjct: 1 MNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPD 60 Query: 73 TFAVLPWTVDGAKSARVICDVYTPDGKPFEGDPRYRLRRMMEKAEQLGYTPYAGPEMEFF 132 T PW +A+++ ++ +G PF DPR LR+++ K +++G T A E+EF+ Sbjct: 61 TLCNEPW--QKRPTAQLLMTMHELEGDPFFADPREVLRQVVAKFDEMGLTICAAFELEFY 118 Query: 133 ILPI-NEKGEPVPEFLDHGG-------YFDLLPLSKVEEIRRDIAIALEKMGITVEATHH 184 ++ N G P P G + + L + + +DI ++ GI +A Sbjct: 119 LIDQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVK 178 Query: 185 EVAPSQHEVDFRYDTF-LRTADNAQTVKLVIKTMAIFHGYHATFMPKPFYGVNGSGMHVH 243 E AP+Q EV+ + ++ D A +K +IK +A H TFM KP+ G G+G+HVH Sbjct: 179 ESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVH 238 Query: 244 MSLFRGDKNAFYDPDDPLGLSKELRYFVGGILKHAKALAAVTNPTINSYKRLVPGYEAPV 303 +S+ D + +DP + LR+ +GG+L+ A A P +NSY+R + P Sbjct: 239 ISILDKDGKNIFASEDP-EQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPN 297 Query: 304 YISWSVGNRSALIRIPKARGKATRLEYRSPDPSCNIYLAFAAILAAGLDGIINKIEPPAP 363 W + NR+ IR+P A R+E+R N YL A++LA G+ NKIEP AP Sbjct: 298 SPCWGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAP 357 Query: 364 VEENIYHMTSERREELNIESLPGSLKEAVEELKKDDVIIDALGEHIFEKFVEAAEKDWKE 423 VE N Y E N +SLP +L++A+ EL +V+ + + FV E + +E Sbjct: 358 VEGNSY--------EQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEE 409 Query: 424 FSTYVTNWELQRYLY 438 F +++ E YL+ Sbjct: 410 FEHSISDLEYNWYLH 424 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: 473 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: 439 Length of database: 426 Length adjustment: 32 Effective length of query: 407 Effective length of database: 394 Effective search space: 160358 Effective search space used: 160358 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 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