Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate 353285 BT3759 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
Query= BRENDA::Q5JFW1 (330 letters) >FitnessBrowser__Btheta:353285 Length = 322 Score = 178 bits (451), Expect = 2e-49 Identities = 122/341 (35%), Positives = 178/341 (52%), Gaps = 37/341 (10%) Query: 1 MIKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRG-LDLRFTNT 59 MIKA ++G +GY GEL+RLL HPE EI I S AG ++ VH L G DLRFT+ Sbjct: 1 MIKAGIIGGAGYTAGELIRLLLNHPETEIVFINSSSNAGNRITDVHEGLYGETDLRFTDQ 60 Query: 60 KEFDA-DVIFLAVPHGTSMEIIDDY--LGSAKIIDMSADFRLREDLYREYYGEHKRPELI 116 DA DV+F HG + + ++ + KIID+S D+R++ D +H Sbjct: 61 LPLDAIDVLFFCTAHGDTKKFMESHNVPEDLKIIDLSMDYRIKSD-------DH------ 107 Query: 117 EEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFRE---LTDEAIVDLKVSSSAGG 173 +F+YGLPEL+R+ A+ VANPGC AT L L P + LT + V+ S+ G Sbjct: 108 -DFIYGLPELNRRATCTAKHVANPGCFATCIQLGLLPLAKNLMLTGDVSVNAITGSTGAG 166 Query: 174 RRENVASIHPERSHVVRVYKPYHHRHEGEVIQET-------GVKAAFTVHSVDIIRGLLA 226 + S R++ + +YK + H+H E+ Q + F + D RG+ A Sbjct: 167 VKPGATSHFSWRNNNISIYKAFDHQHVPEIKQSLKQLQNSFDSEIDFIPYRGDFPRGIFA 226 Query: 227 TIYFRFEGSTRELLRKL-LVYKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGFAHDEE 285 T+ + + + E++R Y + FV +V DK D K V+ +N I ++ Sbjct: 227 TLVVKTKVALEEIVRMYEEYYAKDSFVHIV-DKN-----IDLKQVVNTNKCLIHL--EKH 278 Query: 286 NSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYP 326 + +++S IDNL+KG SGQAV NMNLMF L+E GL P Sbjct: 279 GDKLLIISCIDNLLKGASGQAVHNMNLMFNLEETVGLRLKP 319 Lambda K H 0.321 0.140 0.404 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: 298 Number of extensions: 21 Number of successful extensions: 5 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: 330 Length of database: 322 Length adjustment: 28 Effective length of query: 302 Effective length of database: 294 Effective search space: 88788 Effective search space used: 88788 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: 48 (23.1 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