Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 233 bits (593), Expect = 3e-65 Identities = 153/465 (32%), Positives = 230/465 (49%), Gaps = 19/465 (4%) Query: 16 GGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCR 75 GG V D + +PA VIA G+ EV+ A++ A+ AF W S +R Sbjct: 524 GGKDVTTDDTIASTNPAKPA--EVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAM 581 Query: 76 ILLEAARIIREREDEIATMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAG-EHIQL 134 L AA I R R E++ + + GK +A D+ L+YYA + + Sbjct: 582 FLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGR 641 Query: 135 PGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAE 194 G + +P G+ I WN+PF IA +A A+ GN ++FKPS L E Sbjct: 642 APGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTE 701 Query: 195 IYSEAGVPPGLFNVVQGGAAT-GQFLCQHPDVAKVSFTGSVPTGMKIMEMSAK------G 247 I+ EAG+P G+FN V G ++ G +L +HP V+ + FTGS+ G++I E +AK Sbjct: 702 IFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQ 761 Query: 248 IKPVTLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEE 307 K V E+GGK+ +II D D++ AV L + F QGQ C +RV V I D+F E Sbjct: 762 CKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVER 821 Query: 308 VVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKL 367 +VK Q IKIG MGP+ + + +L +VKVA+++G ++ DI Sbjct: 822 LVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPA------ 875 Query: 368 KDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRD 427 +G Y+ ++ + +EEIFGPV++++ E L AN T F L GVF+R Sbjct: 876 -EGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRS 934 Query: 428 IQRAHRVVAELQAGTCFINNYNVSPV--ELPFGGYKKSGFGRENG 470 + + E + G ++N + + PFGG+K SG G + G Sbjct: 935 PENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTG 979 Lambda K H 0.320 0.137 0.411 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: 1129 Number of extensions: 56 Number of successful extensions: 7 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: 494 Length of database: 1013 Length adjustment: 39 Effective length of query: 455 Effective length of database: 974 Effective search space: 443170 Effective search space used: 443170 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