Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate PP_5299 PP_5299 glutamate-putrescine ligase
Query= reanno::WCS417:GFF5301 (458 letters) >FitnessBrowser__Putida:PP_5299 Length = 460 Score = 812 bits (2098), Expect = 0.0 Identities = 393/458 (85%), Positives = 425/458 (92%), Gaps = 1/458 (0%) Query: 2 SVPPRAVQLNEANAFLKDHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASL 61 SV P A +E N FL+ HP+ YVDLLI+DMNGVVRGKRIER SLHKVYEKGINLPASL Sbjct: 3 SVTPCASSSSEMNDFLQAHPDTQYVDLLISDMNGVVRGKRIERASLHKVYEKGINLPASL 62 Query: 62 FALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFA 121 FALDINGSTVESTGLGLDIGDADRIC+PIP TL +EPWQKRPTAQLLMTMHEL+G+PFFA Sbjct: 63 FALDINGSTVESTGLGLDIGDADRICFPIPGTLSDEPWQKRPTAQLLMTMHELDGQPFFA 122 Query: 122 DPREVLRQVVSKFDDLGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYLI 181 DPREVLRQVVSKFDDLGLTICAAFELEFYLIDQ+N+NGRPQPPRSPISGKRP STQVYLI Sbjct: 123 DPREVLRQVVSKFDDLGLTICAAFELEFYLIDQDNLNGRPQPPRSPISGKRPQSTQVYLI 182 Query: 182 DDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLI 241 DDLDEY DCLQD+LE AKEQG+PADAIVKESAPAQFEVNLHHVADP+KACDYA+LLKRLI Sbjct: 183 DDLDEYADCLQDMLEAAKEQGLPADAIVKESAPAQFEVNLHHVADPLKACDYAILLKRLI 242 Query: 242 KNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILD-KDGKNIFASEDPEQNAALRHAIGGV 300 KN+AYDHEMDTTFMAKPYPGQAGNGLHVHIS+LD K GKNIFAS+DP Q+ LRHAIGGV Sbjct: 243 KNVAYDHEMDTTFMAKPYPGQAGNGLHVHISLLDKKTGKNIFASDDPLQSDTLRHAIGGV 302 Query: 301 LETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSDAVRIEHRVAG 360 LET+PA MAFLCPN+NSYRRFGAQFYVPN+P WGLDNRTVA+RVPT SS+ VR+EHRVAG Sbjct: 303 LETMPASMAFLCPNINSYRRFGAQFYVPNAPSWGLDNRTVAVRVPTDSSENVRLEHRVAG 362 Query: 361 ADANPYLLMASVLAGVHHGLTNKIEPNAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMA 420 ADANPYL++A++LAGVHHGLTNK+EP AP+EGNSYEQ EQSLPNNLRDALR LDDSEV+ Sbjct: 363 ADANPYLMLAAILAGVHHGLTNKVEPEAPIEGNSYEQLEQSLPNNLRDALRALDDSEVLN 422 Query: 421 KYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV 458 +YI P YIDIFVACKESEL EFE SISDLEYNWYLHTV Sbjct: 423 QYISPDYIDIFVACKESELAEFEVSISDLEYNWYLHTV 460 Lambda K H 0.318 0.137 0.409 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: 874 Number of extensions: 22 Number of successful extensions: 2 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: 458 Length of database: 460 Length adjustment: 33 Effective length of query: 425 Effective length of database: 427 Effective search space: 181475 Effective search space used: 181475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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