Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF1137 PGA1_c11520 gamma-glutamylputrescine synthetase PuuA
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Phaeo:GFF1137 Length = 452 Score = 461 bits (1186), Expect = e-134 Identities = 221/438 (50%), Positives = 290/438 (66%) Query: 7 FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTG 66 +L+ R+ E+E II D+ GIARGK +P SKF + LP ++ QT+TGD+ E G Sbjct: 15 YLEGRRLDEVECIISDLPGIARGKAVPASKFAKQDYFHLPDSIFYQTITGDWAEAADDDG 74 Query: 67 VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGW 126 + DM+ PD ST PW D T QVIHD D P+ SPR VL+RV++LY KGW Sbjct: 75 WIEKDMILKPDMSTATAAPWTGDWTLQVIHDAYDRDHKPIPFSPRNVLKRVVQLYHDKGW 134 Query: 127 KPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCE 186 +PV+APE+EF+LV N DP ++P +GR+GRP RQAYS+ AV+EF P+ +DIY++ E Sbjct: 135 QPVVAPEMEFFLVARNIDPAREIEPMMGRSGRPAAARQAYSMTAVDEFGPVIDDIYDFAE 194 Query: 187 VQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPME 246 Q E+D + E GA Q+EIN HGDP+KLAD VF FKR +REAALRH +ATFMAKP+ Sbjct: 195 AQGFEIDGITQEGGAGQLEINLRHGDPVKLADEVFYFKRLIREAALRHDCFATFMAKPIA 254 Query: 247 GEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYR 306 EPGSAMH+H S++D E+G N+F+GP G T F +I GLQ + PA + + APY+NSYR Sbjct: 255 DEPGSAMHIHHSIIDMESGDNIFSGPQGGETDAFYHFIGGLQNHLPAGLAVMAPYVNSYR 314 Query: 307 RLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLG 366 R + AAPIN+ W DNRT G R+P SGP ARR+ENRI G+DCNPYL IA +LA GYLG Sbjct: 315 RYVKEQAAPINLEWARDNRTTGIRVPLSGPEARRVENRIAGMDCNPYLGIALSLACGYLG 374 Query: 367 MTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426 + + + D Y +P+ + + L L + EVLG +F + Y +K EY+ Sbjct: 375 LVNEERPRKQFKGDAYAGDGDIPQVMGQALDLFEEASALHEVLGPEFARVYSIVKRAEYD 434 Query: 427 AFFRVISSWERRHLLLHV 444 F +VIS WER HLLL+V Sbjct: 435 EFLQVISPWEREHLLLNV 452 Lambda K H 0.321 0.138 0.418 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: 632 Number of extensions: 19 Number of successful extensions: 1 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: 444 Length of database: 452 Length adjustment: 33 Effective length of query: 411 Effective length of database: 419 Effective search space: 172209 Effective search space used: 172209 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 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