Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 229 bits (583), Expect = 5e-64 Identities = 155/469 (33%), Positives = 233/469 (49%), Gaps = 24/469 (5%) Query: 47 DAVSRKTFPTVNPST-GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLL 105 D + T + NP+ EVI +V +G K +VD A++AA+ AF WR + R L Sbjct: 527 DVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPA---WRDTSPADRAMFL 583 Query: 106 NRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAG-----WADKYHGKT 160 +R AD+ R L+A + L+ GK + ++ D+ + L YYA + G+ Sbjct: 584 HRAADIARRRMFELSAWQVLEVGKQWDQAFH-DVGEGIDFLDYYAHEMLRLGTPRRMGRA 642 Query: 161 IPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALY 220 G+ ++ ++P G+ I PWNFP + A+ TGN V+ K + Sbjct: 643 ---PGEL-NHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYN 698 Query: 221 VANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQ-----VAAG 275 + + +EAG P GV N VPG G + H V + FTGS E+G IQ V G Sbjct: 699 LTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPG 758 Query: 276 SSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEF 335 KRV E+GGK+ II DAD+D AV Q ++ F QGQ C A SR V + IYD F Sbjct: 759 QMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRF 818 Query: 336 VERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRG 395 VER V A++ +G D GP D + K IL Y+ +QEG L+ I A+ G Sbjct: 819 VERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAE-G 877 Query: 396 YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDK 455 ++ T+ ++ IA+EEIFGPV+ +++ +E + AN + + L VF++ + Sbjct: 878 CYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPEN 937 Query: 456 ANYLSQALQAGTVWVN--CYDVFGAQSPFGGYKMSGSGRELG--EYGLQ 500 + + G +++N + PFGG+KMSG G + G +Y LQ Sbjct: 938 LTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTGGPDYLLQ 986 Lambda K H 0.319 0.136 0.409 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: 1190 Number of extensions: 65 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: 517 Length of database: 1013 Length adjustment: 40 Effective length of query: 477 Effective length of database: 973 Effective search space: 464121 Effective search space used: 464121 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: 55 (25.8 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