Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate BPHYT_RS09955 BPHYT_RS09955 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS09955 Length = 445 Score = 580 bits (1494), Expect = e-170 Identities = 265/442 (59%), Positives = 343/442 (77%) Query: 3 DIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDG 62 D+ +FL+ +R+ E+E +IPDM G+ARGKI+P++ F S M + A+++ TV G++ Sbjct: 4 DLREFLEHHRIHEVECVIPDMTGVARGKIVPKNLFLSEGKMHMSNALLMITVNGEFANFE 63 Query: 63 TLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYK 122 G +DPDMVC+PD +T+R++PWA++ A VIHDCV DG P+ ISPR VLRRVL LY+ Sbjct: 64 RFVGPSDPDMVCIPDPNTVRLVPWAIEQVAVVIHDCVGLDGKPIGISPRAVLRRVLRLYE 123 Query: 123 AKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIY 182 A+GW+PV+APE+EFYL+ NK+P PL+PP+GR GR E GRQ++SI+AVNEFDP F+D+ Sbjct: 124 ARGWRPVVAPEMEFYLIAQNKNPHEPLRPPLGRAGRHEAGRQSFSIDAVNEFDPFFQDLS 183 Query: 183 EYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMA 242 +CE+ +L V+TL+HEVGA QMEINF HGD L LAD VFLFKR VRE A RH ++ATFMA Sbjct: 184 RFCEMTQLGVETLVHEVGAGQMEINFSHGDALDLADRVFLFKRAVRETAFRHGIFATFMA 243 Query: 243 KPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYI 302 KPME EPGSAMH+HQS+VD E+G N+F+ PDG + LF +YI GLQKY P MP+FAPY+ Sbjct: 244 KPMEHEPGSAMHIHQSIVDRESGQNIFSLPDGSASPLFFNYIGGLQKYMPQAMPMFAPYV 303 Query: 303 NSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAA 362 NSYRRLSRF AAPINV WGYDNRT G R+P+S P RR+ENR+PGVD NPYLA+AATLA Sbjct: 304 NSYRRLSRFTAAPINVRWGYDNRTCGIRVPNSEPDGRRLENRVPGVDVNPYLAMAATLAC 363 Query: 363 GYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKE 422 GYLGM ++ EA+ P++ Y+L Y+LPR LE+ L + C +AEVLG+ FV+AY A+KE Sbjct: 364 GYLGMVEQQEASAPMIESAYDLEYELPRGLEDALKALSKCTELAEVLGDSFVQAYCAVKE 423 Query: 423 TEYEAFFRVISSWERRHLLLHV 444 E+E F + I++WER HL L V Sbjct: 424 KEFETFSQGITAWEREHLQLLV 445 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: 644 Number of extensions: 20 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: 445 Length adjustment: 32 Effective length of query: 412 Effective length of database: 413 Effective search space: 170156 Effective search space used: 170156 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