Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= metacyc::MONOMER-20632 (478 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 274 bits (700), Expect = 1e-77 Identities = 167/462 (36%), Positives = 237/462 (51%), Gaps = 11/462 (2%) Query: 8 YIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSD 67 +IGG+ V D S NP+ +V+A+V GG+ EVDAA++AA+KAFPAW D SP R+ Sbjct: 522 FIGGKDVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAM 581 Query: 68 LLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLEST 127 L + R ++ E GK + + Y+A E LR Sbjct: 582 FLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGR 641 Query: 128 RPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLAD 187 PG + Q G+ +I PWNFP AI AA A+ GN V+ KP+ L + Sbjct: 642 APGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTE 701 Query: 188 IMAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQ----- 241 I E G P GVFN + GR S MGD L++H V + FTGS VG ++ A Q Sbjct: 702 IFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQ 761 Query: 242 -ARVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVAL 300 RV EMGGKN +I+ DDADL+ AV L +F GQ+C+A SR+IV D I+D+FV Sbjct: 762 CKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVER 821 Query: 301 LAEKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGW 360 L + A+++G + DP +GP + Y+ +A EG +V R + G Sbjct: 822 LVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLV---KRTDIPAEGC 878 Query: 361 YVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHA 420 YV T++ + RI EE+FGPV + +R +++EAL IANG F L+ G+ + S ++ Sbjct: 879 YVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENL 938 Query: 421 RHFQRYARAGMTMVNLATAG-VDYHVPFGGTKSSSYGAREQG 461 +R R G +N + G + PFGG K S G++ G Sbjct: 939 TKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTGG 980 Lambda K H 0.317 0.133 0.384 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: 1072 Number of extensions: 54 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 1013 Length adjustment: 39 Effective length of query: 439 Effective length of database: 974 Effective search space: 427586 Effective search space used: 427586 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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