Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF1139 PGA1_c11540 gamma-glutamylputrescine synthetase PuuA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_925 (458 letters) >FitnessBrowser__Phaeo:GFF1139 Length = 448 Score = 276 bits (707), Expect = 8e-79 Identities = 156/434 (35%), Positives = 228/434 (52%), Gaps = 4/434 (0%) Query: 26 VDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADR 85 + + D+NG +RGKR+ K+ + +P S +D+ G VE L + GDAD Sbjct: 18 IRIAACDLNGQMRGKRMPVGLADKLADGAARMPISTLNVDLWGRDVEDNPLVFETGDADG 77 Query: 86 ICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLANVVRKFDEMGLTICAAF 145 + P PW P+A + M M+ +G PF DPR VLA+V+ ++ + G + AA Sbjct: 78 VMLPTERGAVPMPWLANPSALVPMAMYWEDGRPFMGDPRHVLADVLARYQQRGWRVVAAT 137 Query: 146 ELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPA 205 E+EF L+D +P PP P++G+ V + +LD + D+ EG+ GIPA Sbjct: 138 EMEFSLLDDSGA--QPAPPIDPLTGRELDQQSVLSVAELDAFDAFFTDLYEGSDAMGIPA 195 Query: 206 DAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGN 265 + + E+ QFE+NL+H + ++A D A L K L+K +A H TFMAKPY +AGN Sbjct: 196 QSAISEAGLGQFEINLNH-QEAMRAADDAWLFKALVKGLARKHGFAATFMAKPYAEEAGN 254 Query: 266 GLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQF 325 G+HVH S+ D+DG N+F + L +A+ G L +PA L P+ NSY R Sbjct: 255 GMHVHFSVEDEDGNNVFNDGTERGSGLLMNAVAGCLTAMPASTLILAPHGNSYDRLVPGA 314 Query: 326 YVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIE 385 + P S W +NRT AIR+P GS A RIEHRVAG D NPYL++A VL G+ + Sbjct: 315 HAPVSAAWAYENRTAAIRIPGGSPKARRIEHRVAGGDINPYLMLAVVLGAALAGIEDGAT 374 Query: 386 PGAPVEGNSYE-QNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEH 444 P AP EGN YE L + + A+ D ++A+ + + I V K E F Sbjct: 375 PPAPSEGNIYEIDGLPQLAPDWKAAIDLFDSDPLIARILPDRVIRNLVMMKRQEQAGFAE 434 Query: 445 SISDLEYNWYLHTV 458 ++ + +L V Sbjct: 435 RPAESHWLSWLEAV 448 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: 569 Number of extensions: 27 Number of successful extensions: 3 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: 448 Length adjustment: 33 Effective length of query: 425 Effective length of database: 415 Effective search space: 176375 Effective search space used: 176375 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