Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 240 bits (613), Expect = 1e-67 Identities = 156/482 (32%), Positives = 248/482 (51%), Gaps = 19/482 (3%) Query: 13 FIGGKFLPCNSYIDSYDPST-GEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSL 71 FIGGK + + I S +P+ EV +V GK E++AA+EAA++AFPAW SP +R++ Sbjct: 522 FIGGKDVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAM 581 Query: 72 VLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQM 131 L+R AD+ + + EL+ + + GK A D+ + ++A L + Sbjct: 582 FLHRAADIARRRMFELSAWQVLEVGKQWDQA-FHDVGEGIDFLDYYAHEMLRLGTPRRMG 640 Query: 132 SHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFC 191 G +++ P GIA +I+PWN P + A AI GN VI KPS + S + Sbjct: 641 RAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLT 700 Query: 192 KLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP------ 245 ++ +AG+P GV N V G +G+ LV HP+V +I FTGS RI + +A Sbjct: 701 EIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQM 760 Query: 246 HCKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLK 305 CK++ E+GGKN II +DA+L+E + + S+F QG+ C SR+ V IY F++ Sbjct: 761 QCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVE 820 Query: 306 RFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPL 365 R V+A + K+G DP+ MG + + + + YV A+ EG + V + +P Sbjct: 821 RLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVL-----VKRTDIPA 875 Query: 366 RNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWS 425 G ++ T++ IK R EEIFGPV V+ + +E + AN R+ L V+S Sbjct: 876 E---GCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFS 932 Query: 426 KDVGRIHRVAKKLQSGLVWTNCWLIREL--NLPFGGMKSSGIG-REGAKDSYDFFTEIKT 482 + + + ++ + G ++ N + PFGG K SG+G + G D F + + Sbjct: 933 RSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTGGPDYLLQFMDPRC 992 Query: 483 IT 484 +T Sbjct: 993 VT 994 Lambda K H 0.319 0.134 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: 1042 Number of extensions: 51 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: 487 Length of database: 1013 Length adjustment: 39 Effective length of query: 448 Effective length of database: 974 Effective search space: 436352 Effective search space used: 436352 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: 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