Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate AZOBR_RS08850 AZOBR_RS08850 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__azobra:AZOBR_RS08850 Length = 447 Score = 573 bits (1476), Expect = e-168 Identities = 269/444 (60%), Positives = 342/444 (77%), Gaps = 3/444 (0%) Query: 4 IDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFES---GESMRLPQAVMIQTVTGDYPE 60 ++DF+KKNR+TE+E ++PDM+GIARGKI+P KF +RLP+A+ +QTVTG+YPE Sbjct: 4 MEDFIKKNRITEVECLVPDMSGIARGKIVPAEKFLRILRDRGLRLPEAIFVQTVTGEYPE 63 Query: 61 DGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLEL 120 D ++T + D+ +PD TIR +PW +PTAQVI DCV+ DG+PV SPR VL+RVL L Sbjct: 64 DDSVTSDENSDIYMIPDERTIRFVPWYEEPTAQVITDCVYADGSPVNFSPRHVLKRVLSL 123 Query: 121 YKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFED 180 Y+ +GWKP++APELEF+LV +NKDPD PL PP+GR GR E+GRQA+ I+AVNEFDP+FE Sbjct: 124 YEERGWKPMVAPELEFFLVQVNKDPDYPLVPPVGRNGRVESGRQAFGIDAVNEFDPIFEM 183 Query: 181 IYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATF 240 +Y++CE Q++++DTL HE GAAQ+EINF HGD L+LAD FLFKRT REAALRH++YATF Sbjct: 184 VYDFCEAQDIDIDTLTHEAGAAQIEINFNHGDALELADQAFLFKRTAREAALRHQVYATF 243 Query: 241 MAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAP 300 MAKPM+ EPGSAMH+HQS+VD ++G NLF+ +G T LF S+IAGLQKY P MP+ AP Sbjct: 244 MAKPMQNEPGSAMHIHQSVVDADSGRNLFSDANGADTPLFMSHIAGLQKYLPYAMPLLAP 303 Query: 301 YINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATL 360 +NSYRRL APINV WG DNRT G R+P S +RR+ENR+ G D NPYLAIAA+L Sbjct: 304 NVNSYRRLVPNSDAPINVHWGRDNRTTGLRVPVSPADSRRVENRVAGADANPYLAIAASL 363 Query: 361 AAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLAL 420 A GYLGM Q LE T+P+ Y L + LPR+ + L AC+P+ EVLGEKF+ A + Sbjct: 364 ACGYLGMAQGLEPTDPVKGSAYRLAFTLPRHQGDALQKFNACKPLKEVLGEKFLDAVTCV 423 Query: 421 KETEYEAFFRVISSWERRHLLLHV 444 KE EYEA+ RVISSWER +LLL+V Sbjct: 424 KEAEYEAYHRVISSWERENLLLNV 447 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: 687 Number of extensions: 26 Number of successful extensions: 2 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: 447 Length adjustment: 32 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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