Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 194 bits (492), Expect = 2e-53 Identities = 131/441 (29%), Positives = 206/441 (46%), Gaps = 13/441 (2%) Query: 23 NPAT-GDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVF 81 NPA +V+ + + +VDAA+ AA AF W T+P RA L + AD+ Sbjct: 538 NPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFEL 597 Query: 82 AELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGV 141 + + GK AF+D + +D ++A L G + + P G+ Sbjct: 598 SAWQVLEVGKQWDQAFHD-VGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGI 656 Query: 142 VASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVINIL 200 A IAPWN+P +A A A+ GN V+ KPS I L E+ ++ P GV N + Sbjct: 657 AAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYV 716 Query: 201 FGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS------SIKRTHMELGGKAPVI 254 GR +GD L HP+V M+ TGS+ G I A KR E+GGK +I Sbjct: 717 PGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAII 776 Query: 255 VFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDD 314 + DDAD++ V V + GQ C+A R+ IYD VE+L A +K G +D Sbjct: 777 IDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSED 836 Query: 315 ESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAI 374 + +GP++ + + + + V+ A+ G KV+ G Y T++ G I Sbjct: 837 PANYMGPVADASLQKNILEYVKVAEQEG--KVLVKRTDIPAEGCYVPLTIVEGIKPHHRI 894 Query: 375 VQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN- 433 Q+E+FGPV++V N ++ + AN +++ L V+++ + + G ++N Sbjct: 895 AQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNR 954 Query: 434 -THFMLVSEMPHGGQKLSGYG 453 + +V P GG K+SG G Sbjct: 955 GSTGAMVERQPFGGFKMSGVG 975 Lambda K H 0.317 0.134 0.397 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: 1002 Number of extensions: 47 Number of successful extensions: 6 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: 474 Length of database: 1013 Length adjustment: 39 Effective length of query: 435 Effective length of database: 974 Effective search space: 423690 Effective search space used: 423690 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