Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_057507762.1 ABB28_RS05950 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >NCBI__GCF_001431535.1:WP_057507762.1 Length = 465 Score = 501 bits (1289), Expect = e-146 Identities = 245/442 (55%), Positives = 310/442 (70%), Gaps = 4/442 (0%) Query: 7 FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDG-TLT 65 +LK R+TE+E ++PD+ GIARGKIIP KF RLP+ + TVTGDYP+D LT Sbjct: 24 WLKDRRITEVECLVPDITGIARGKIIPADKFSHDYGTRLPEGIFATTVTGDYPDDYYELT 83 Query: 66 GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKG 125 +D DMV PD T+RM+PWA DPTAQ+IHDC G P ++PR VLRRVL+ Y G Sbjct: 84 SPSDSDMVLRPDPETVRMVPWATDPTAQIIHDCYTKSGQPHELAPRNVLRRVLDAYTELG 143 Query: 126 WKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYC 185 +PV+APELEF+LV N DPD PL PP GR+GRPET RQ+YSI+AVNEFDP+ + +Y+Y Sbjct: 144 LRPVVAPELEFFLVQKNTDPDFPLLPPAGRSGRPETARQSYSIDAVNEFDPILDLMYDYA 203 Query: 186 EVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPM 245 + +L+VDTLIHE GAAQ+E+NF H + LAD VFLFKRT+REAA+RH +YATF+AKPM Sbjct: 204 DAMKLDVDTLIHESGAAQLEVNFTHAGAMNLADQVFLFKRTMREAAMRHGVYATFLAKPM 263 Query: 246 EGEPGSAMHMHQSLVDEETGHNLFTGP---DGKPTSLFTSYIAGLQKYTPALMPIFAPYI 302 E EPGSAMH+HQSL+ G N+F G +G+ + +F Y+ GLQK+ P M FAP + Sbjct: 264 ENEPGSAMHIHQSLLRISDGANVFAGDGDGEGEFSPVFGHYLGGLQKFAPQAMAFFAPNV 323 Query: 303 NSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAA 362 NSYRRL +P NV WG+DNRT G R+P P R+E+R G D NPYLA+AATLA Sbjct: 324 NSYRRLVFGEVSPSNVHWGFDNRTCGLRVPMDTPDNMRVESRFAGSDANPYLAMAATLAC 383 Query: 363 GYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKE 422 G LG+ +L P+ EL Y LPR+L E L + C + +LGE+F +AY+++K Sbjct: 384 GLLGLRGQLAPDAPVSGSAKELGYDLPRSLGEALDGLEQCAELQALLGERFCRAYISVKR 443 Query: 423 TEYEAFFRVISSWERRHLLLHV 444 EYE FFRVISSWER LLL+V Sbjct: 444 KEYETFFRVISSWEREFLLLNV 465 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: 700 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: 444 Length of database: 465 Length adjustment: 33 Effective length of query: 411 Effective length of database: 432 Effective search space: 177552 Effective search space used: 177552 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 24 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