Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate HSERO_RS15690 HSERO_RS15690 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__HerbieS:HSERO_RS15690 Length = 471 Score = 132 bits (333), Expect = 2e-35 Identities = 129/460 (28%), Positives = 191/460 (41%), Gaps = 54/460 (11%) Query: 8 LKKNRVTEIEAIIPDMAGIARGKIIPRS-----KFESGESMRLPQAVMIQTVTGDYPEDG 62 +K N V ++ D G + +P S KFESG + D Sbjct: 12 VKDNEVKFVDFRFADTRGKEQHVSVPVSHFDIDKFESGHAF-------------DGSSIA 58 Query: 63 TLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVH-FDGTPVAISPRRVLRRVLELY 121 G+ DM+ +PD +T + P+ + T + D + DG PR + +R Sbjct: 59 GWKGIEASDMLLIPDPNTANIDPFMEETTLFMQCDVIEPSDGKGYDRDPRSIAKRAEAYL 118 Query: 122 KAKGWKPV--IAPELEFYLVDM---------------NKDPDLPLQPPI--GRTGRPETG 162 K+ G PE EF++ D +++ I G +G T Sbjct: 119 KSSGLGDTAYFGPEPEFFIFDGVRWGADMSGSFVKIDSEEASWSTGAKIEGGNSGHRPTV 178 Query: 163 RQAY-SIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEV-GAAQMEINFMHGDPLKLADSV 220 + Y + V+ F + ++ E + V+ HEV GA Q E+ ++ AD Sbjct: 179 KGGYFPVPPVDSFQDMRSEMSLIIESLGIPVEVHHHEVAGAGQNELGTKFSTLVERADWT 238 Query: 221 FLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLF 280 K + A + ATFM KP+ G+ GS MH+HQS+ + G NLF G S F Sbjct: 239 QTMKYVIWNVAHTYGKTATFMPKPLVGDNGSGMHVHQSVWKD--GKNLFAGDGYAGLSEF 296 Query: 281 TSY-IAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH-SGPAA 338 Y I G+ K+ AL I P NSY+RL AP+ +A+ NR+ RIPH + P Sbjct: 297 ALYYIGGIIKHAKALNAITNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPHVANPKG 356 Query: 339 RRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPR-------N 391 RRIE R P NPYL +A L AG G+ K+ E D Y LP + + + Sbjct: 357 RRIETRFPDPLANPYLCFSALLMAGLDGVQNKIHPGEAATKDLYHLPPEEDKLIPTVCSS 416 Query: 392 LEEGLTLMGACEPI---AEVLGEKFVKAYLALKETEYEAF 428 L+E L + V + + AY+ LK E + F Sbjct: 417 LDEALEHLDKDREFLTRGGVFTDSMIDAYIDLKMQEVQRF 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: 513 Number of extensions: 32 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: 471 Length adjustment: 33 Effective length of query: 411 Effective length of database: 438 Effective search space: 180018 Effective search space used: 180018 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