Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 3608834 Dshi_2226 Glutamate--putrescine ligase (RefSeq)
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Dino:3608834 Length = 456 Score = 466 bits (1200), Expect = e-136 Identities = 225/438 (51%), Positives = 293/438 (66%), Gaps = 1/438 (0%) Query: 7 FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTG 66 +L+ R+ E+E I+ D+AG+ARGK +P +KF S LP ++ QT+TG + E L G Sbjct: 20 YLEGRRLDEVECIVADLAGVARGKAMPAAKFARQMSFYLPNSIFFQTITGGWAE-AALDG 78 Query: 67 VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGW 126 T+PDMV PD ST PW D T Q+IHD G P+ ++PR VL+RV+ LYKA+GW Sbjct: 79 FTEPDMVLKPDFSTATPAPWTADWTLQIIHDIEDQSGAPMPVAPRNVLKRVIALYKARGW 138 Query: 127 KPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCE 186 KPV+APE+EFYL N DP + +QPP+GRTGR RQAYS+ AV+E+ P+ +DIY++ E Sbjct: 139 KPVVAPEMEFYLTARNIDPAIAIQPPMGRTGRRAAARQAYSMSAVDEYGPVIDDIYDFAE 198 Query: 187 VQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPME 246 Q LE+D + E GA Q+EIN HGDPLKLAD VF FKR +REAALRH +ATFMAKP++ Sbjct: 199 AQGLEIDGITQEGGAGQIEINLRHGDPLKLADEVFYFKRLIREAALRHDCFATFMAKPIQ 258 Query: 247 GEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYR 306 EPGSAMH+H S+ D TG N+FT PDG T F +IAGLQ + ++P++APY+NSYR Sbjct: 259 DEPGSAMHIHHSVTDIATGENIFTAPDGTETPAFQHFIAGLQSHLGDVVPLYAPYVNSYR 318 Query: 307 RLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLG 366 R AAPIN+ W DNRT G R+P + PAARR+ENR+ G+DCNPYL IAA+LA GYLG Sbjct: 319 RYVPENAAPINLEWARDNRTAGLRVPVANPAARRVENRLAGMDCNPYLGIAASLACGYLG 378 Query: 367 MTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426 + + + D Y L L L L + ++LG +F + Y +K EY Sbjct: 379 LLAEKPPKPQYVGDAYSGSEDLAPELGAALDLFSEATAVHDILGPEFCRVYEIVKRHEYT 438 Query: 427 AFFRVISSWERRHLLLHV 444 F +VIS WER HLLL+V Sbjct: 439 EFLQVISPWEREHLLLNV 456 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: 671 Number of extensions: 26 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: 444 Length of database: 456 Length adjustment: 33 Effective length of query: 411 Effective length of database: 423 Effective search space: 173853 Effective search space used: 173853 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