Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate CCNA_03230 CCNA_03230 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Caulo:CCNA_03230 Length = 465 Score = 551 bits (1421), Expect = e-161 Identities = 268/446 (60%), Positives = 329/446 (73%), Gaps = 3/446 (0%) Query: 1 MHDIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPE 60 + + D+ + + EIE ++PD+AG+ARGKI+P KF SM LP AV QT+TGD+PE Sbjct: 21 IEEAKDWFARQHIEEIECVVPDLAGVARGKIMPVRKFLGSPSMNLPLAVFYQTITGDFPE 80 Query: 61 -DGTLTGV-TDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVL 118 +G + V +D D+ PD +T+ +PWA DPTAQVIHD H DG PV +PR+VLRRVL Sbjct: 81 FEGAVNAVQSDTDIFLTPDFATLAAVPWAQDPTAQVIHDAFHPDGRPVEEAPRQVLRRVL 140 Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLF 178 LY KGW P++APE+EFYLVD N DPD PL+PPIGR+GRPETGRQ YSI AVNEFD LF Sbjct: 141 ALYADKGWHPIVAPEIEFYLVDRNTDPDYPLKPPIGRSGRPETGRQGYSISAVNEFDALF 200 Query: 179 EDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYA 238 ED+YEY E Q LE+DTLIHE G AQMEIN HG PL+LAD VF+ KRT+REAAL H++YA Sbjct: 201 EDMYEYSERQGLEIDTLIHESGVAQMEINLQHGHPLELADQVFMMKRTIREAALEHEIYA 260 Query: 239 TFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIF 298 TFMAKPM EPGSAMH+HQS+VD++ G NLF+ DG +++F +IAG Q Y PA+M I Sbjct: 261 TFMAKPMANEPGSAMHIHQSIVDKK-GRNLFSDEDGAESAMFHGFIAGQQTYLPAIMAIL 319 Query: 299 APYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAA 358 APY+NSYRR+SR AP+N WGYDNRT G R+P SGP RR+ENRIP D NPYLAIAA Sbjct: 320 APYVNSYRRISRDSGAPVNTQWGYDNRTCGLRVPPSGPNNRRVENRIPSSDANPYLAIAA 379 Query: 359 TLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYL 418 +LAAGYLGM Q L+ +EP+ D +LPR+L + L L AC+P+ E+LG F AY Sbjct: 380 SLAAGYLGMVQGLKPSEPVSIDAGARGIELPRSLSDSLRLFVACQPLVEILGPTFCAAYD 439 Query: 419 ALKETEYEAFFRVISSWERRHLLLHV 444 +K+ EYE F R IS WER LLL+V Sbjct: 440 RVKQAEYETFMRTISPWEREFLLLNV 465 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: 674 Number of extensions: 20 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: 465 Length adjustment: 33 Effective length of query: 411 Effective length of database: 432 Effective search space: 177552 Effective search space used: 177552 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