Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate BWI76_RS00400 BWI76_RS00400 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Koxy:BWI76_RS00400 Length = 469 Score = 132 bits (333), Expect = 2e-35 Identities = 125/403 (31%), Positives = 174/403 (43%), Gaps = 48/403 (11%) Query: 62 GTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAIS--PRRVLRRVLE 119 G G+ + DMV +PDA+T + P+ +PT + D + GT PR + +R E Sbjct: 56 GGWKGINESDMVLMPDATTALIDPFYEEPTLIIRCDILE-PGTLQGYDRDPRSIAKRAEE 114 Query: 120 LYKAKGWKPVI--APELEFYLVDMNKDPDLPLQPPI----------------------GR 155 ++ G + PE EF+L D D+ I G Sbjct: 115 YLRSTGLADTVLFGPEPEFFLFD-----DIRFGASISGSHVAIDDIEGAWNSSTKYEGGN 169 Query: 156 TG-RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA-QMEINFMHGDP 213 G RP + + V+ + + E L V+ HEV A Q EI Sbjct: 170 KGHRPGVKGGYFPVPPVDSSQDIRSTMCMIMEEMGLVVEAHHHEVATAGQNEIATRFNTM 229 Query: 214 LKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPD 273 K AD + ++K V A R ATFM KPM G+ GS MH H SL + G NLF+G Sbjct: 230 TKKADEIQIYKYVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSL--SKNGVNLFSGDK 287 Query: 274 GKPTS-LFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIP 332 S YI G+ K+ A+ + P NSY+RL AP+ +A+ NR+ RIP Sbjct: 288 YAGLSEQALYYIGGVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIP 347 Query: 333 -HSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELP------ 385 + P ARRIE R P NPYL AA L AG G+ K+ E + + Y+LP Sbjct: 348 VVTSPKARRIEVRFPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKE 407 Query: 386 -YQLPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLALKETE 424 Q+ +LEE L + A V + AY+AL+ E Sbjct: 408 IPQVAGSLEEALNALDADREFLTAGGVFTNDAIDAYIALRIEE 450 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: 488 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 469 Length adjustment: 33 Effective length of query: 411 Effective length of database: 436 Effective search space: 179196 Effective search space used: 179196 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