Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_068170530.1 HTA01S_RS10525 glutamine synthetase family protein
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >NCBI__GCF_001592305.1:WP_068170530.1 Length = 456 Score = 560 bits (1443), Expect = e-164 Identities = 267/446 (59%), Positives = 331/446 (74%), Gaps = 3/446 (0%) Query: 2 HDIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPED 61 +D++++L ++RVTE+E ++PD+ G+ARGKI+PR KF MRLPQA++ VTG++PE Sbjct: 11 NDLENWLNEHRVTEVECLVPDLTGVARGKILPREKFTEDRGMRLPQAIVGMGVTGEFPES 70 Query: 62 GTLTGVTDP---DMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVL 118 G V DP DM PD +T+R++PWA DPTAQVIHDC G V +PR VLRR+ Sbjct: 71 GPYYDVVDPTDKDMQLRPDPTTVRIVPWATDPTAQVIHDCFDHHGKLVPFAPRSVLRRIC 130 Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLF 178 +LY A+GW+PV+APELEFYL N DP+ L+PPIGR+GR ET RQAYSI+AVNEFDPLF Sbjct: 131 DLYAAEGWEPVVAPELEFYLTARNTDPNTLLKPPIGRSGRAETSRQAYSIDAVNEFDPLF 190 Query: 179 EDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYA 238 E+IY+YC+ EL VDTLIHEVGA QMEINF H PL LAD VF FKRTVREAALRH MYA Sbjct: 191 EEIYDYCDKMELNVDTLIHEVGAGQMEINFFHAHPLGLADEVFFFKRTVREAALRHDMYA 250 Query: 239 TFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIF 298 TFMAKP+ GEPGSAMH+HQS++D+ TG N+F+ DG + F YI GLQ+Y PA M + Sbjct: 251 TFMAKPIAGEPGSAMHVHQSILDKATGKNIFSNEDGTASESFYHYIGGLQRYIPAAMVLV 310 Query: 299 APYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAA 358 APY+NSYRRLSR AAPIN+ WG+DNRTVG R P S PAARR+ENR+ G D NPY+A+A Sbjct: 311 APYVNSYRRLSRHTAAPINIEWGHDNRTVGIRSPISSPAARRVENRVIGADANPYVAMAM 370 Query: 359 TLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYL 418 TLA GYLGM K++ + D Y PY LPR+L E L + + EVLG++F+ Y Sbjct: 371 TLACGYLGMKNKIKPKPEMKGDAYLAPYSLPRSLGEALDWLRREPDLHEVLGKEFITIYT 430 Query: 419 ALKETEYEAFFRVISSWERRHLLLHV 444 +KE E++ F +VIS WER HLLLHV Sbjct: 431 EIKELEFDEFMKVISPWEREHLLLHV 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: 723 Number of extensions: 31 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: 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 Apr 09 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