Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate 8500980 DvMF_1717 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
Query= curated2:A0RWW0 (348 letters) >FitnessBrowser__Miya:8500980 Length = 350 Score = 267 bits (682), Expect = 3e-76 Identities = 144/351 (41%), Positives = 207/351 (58%), Gaps = 8/351 (2%) Query: 1 MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFT--DLTFSE 58 ++ G+VG +GY G E RLL HP++ + TSR G L + P LRG + + Sbjct: 4 IRAGLVGVTGYTGMELTRLLAGHPNMRLVRATSRTEAGRPLSDIYPFLRGLPGGNAVMTA 63 Query: 59 LDYDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHP 118 D D L+D+CD+ F AVPHG A ++ L R ++V+DLSAD+RL DP Y WY H Sbjct: 64 PDPDDLADNCDVAFLAVPHGAAMEMGATLRQRGLRVVDLSADFRLRDPDVYEAWYKVPHT 123 Query: 119 HPDYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKI 178 L ++V+G+PEL+ + ++ A LV+ PGC +IL L ++ GLV+T+ IVVD+K Sbjct: 124 RRAELPQAVYGLPELYGDAVKKAGLVANPGCYPTATILGLYAALKHGLVETDGIVVDAKS 183 Query: 179 GSSGAG--AGAGTAHAMRAGVIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVV 236 G++GAG A GT + R Y KHRHT EIEQELS IAG + VS +PH + + Sbjct: 184 GATGAGRKAAVGTLFCEVSDTFRAYNIGKHRHTPEIEQELSAIAGTSMVVSFNPHLLPIN 243 Query: 237 RGILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDI 296 RGIL T + L + S +D+ + Q + R+VR++ + P+ + + G+ FCD+ Sbjct: 244 RGILATIYAKLAKPVSPQDVQAAFEQTWQGSRWVRVL----PAGQLPETRHVRGTMFCDV 299 Query: 297 GFDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 G D+ NRLV +SA DNL +GA+G A+ N N+M GL +GL PL P Sbjct: 300 GVVTDQRTNRLVILSAIDNLCRGASGQAVANANLMFGLPVETGLMLAPLMP 350 Lambda K H 0.320 0.137 0.412 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: 291 Number of extensions: 14 Number of successful extensions: 4 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: 348 Length of database: 350 Length adjustment: 29 Effective length of query: 319 Effective length of database: 321 Effective search space: 102399 Effective search space used: 102399 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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