Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_002720541.1 RSPH17029_RS10230 glutamine synthetase family protein
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >NCBI__GCF_000015985.1:WP_002720541.1 Length = 451 Score = 464 bits (1193), Expect = e-135 Identities = 221/438 (50%), Positives = 296/438 (67%), Gaps = 1/438 (0%) Query: 7 FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTG 66 ++ RV E+E I+ D+AG+ARGK +P KF S LP ++ +QT+TG++ D Sbjct: 15 YIADRRVDEVECILSDIAGVARGKAMPAFKFGKQSSFFLPNSIFLQTITGEWA-DNPSGA 73 Query: 67 VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGW 126 T+PDM+ +PD ST PW D T QVIHD V G PV +SPR VLRRV+ELY A+GW Sbjct: 74 FTEPDMILIPDYSTATAAPWTADITLQVIHDAVDQQGRPVPVSPRNVLRRVVELYNAEGW 133 Query: 127 KPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCE 186 P++APE+EF+LV N DP++P+ PP+GRTGR +QAYS+ AV+E+ + +DIY++ E Sbjct: 134 TPIVAPEMEFFLVARNIDPNMPVMPPMGRTGRRAAAKQAYSMSAVDEYGKVIDDIYDFAE 193 Query: 187 VQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPME 246 Q E+D ++ E GA Q+EIN HGDP+ LAD +F FKR +REAALRH +ATFMAKP+E Sbjct: 194 AQGFEIDGILQEGGAGQVEINLAHGDPVALADQIFFFKRLIREAALRHDCFATFMAKPIE 253 Query: 247 GEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYR 306 GEPGSAMH+H S+VD + N+F+ G T F +IAG+Q + PA + + APY+NSYR Sbjct: 254 GEPGSAMHIHHSVVDSASKLNIFSDAKGGETEAFLHFIAGMQTHLPAAVALLAPYVNSYR 313 Query: 307 RLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLG 366 R AAPIN+ WG DNRT G R+P SGP ARR+ENR+ G+DCNPYL +AA+LA GYLG Sbjct: 314 RYVPDFAAPINLEWGRDNRTTGLRVPISGPEARRLENRLAGMDCNPYLGLAASLACGYLG 373 Query: 367 MTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426 + ++ D Y LP NL + L L+ + +VLG +F Y ++K EY+ Sbjct: 374 LKERKMPQPECTGDAYMSETDLPYNLGDALDLLEEDAALRDVLGPEFCGVYDSVKRNEYK 433 Query: 427 AFFRVISSWERRHLLLHV 444 F +VIS WER HLLL+V Sbjct: 434 EFLQVISPWEREHLLLNV 451 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: 612 Number of extensions: 25 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: 451 Length adjustment: 33 Effective length of query: 411 Effective length of database: 418 Effective search space: 171798 Effective search space used: 171798 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 Apr 10 2024. 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