Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 352642 BT3115 putative proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydraogenase (NCBI ptt file)
Query= BRENDA::Q65NN2 (516 letters) >FitnessBrowser__Btheta:352642 Length = 1106 Score = 209 bits (532), Expect = 4e-58 Identities = 151/510 (29%), Positives = 241/510 (47%), Gaps = 28/510 (5%) Query: 6 KHEPFTNFGIEENRKAFEKALETVNNEWLGQS--YPLVIDGERYETENKIVSINPANKEE 63 K+EP T+F + +N++ + Q PL I E E++ + +E Sbjct: 444 KNEPDTDFDLPQNQEWVRSIFSKWKKDGTEQPEIIPLQIGAETVVCESRYPYTDRCQDDE 503 Query: 64 V-VGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVK 122 V + +S+A EK I+ A WR T EER +++ A ++ + + + Sbjct: 504 VCICEMSQADSAQVEKIIEIAEADPAGWRKTTLEERHRIMYEAANRLADMRGDLIGCMCA 563 Query: 123 EAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTGVTVVIPPW 182 GK E D + +EA+D+ +Y M + A V + P G +VI PW Sbjct: 564 VTGKTVIEGDVEVSEAVDYARFYTTAMKKFAALDDVEMK----------PKGTILVISPW 613 Query: 183 NFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEV 242 NF AI G VA + GNTV+LKPA+ A +A F + ++G+PK + + + E Sbjct: 614 NFPCAIPVGGIVAGLAGGNTVILKPATVAAPVAWMFAKAFWDAGVPKEALQVII-TRREA 672 Query: 243 GDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDI 302 L P I TG GT + AK P + AE GGK+ +++ D Sbjct: 673 LKVLTTAPAIKHIILTG----GTDTAQNIAKANP----TTPLSAETGGKNVIILTASGDR 724 Query: 303 ELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDE--VLKRVIEITESKKVGEPDSADVYM 360 + A +I TSAFG AGQKCSA S +V VY++ ++ + S K G +A + Sbjct: 725 DHAIMNIVTSAFGNAGQKCSACSLLLVERSVYEDENFRSKLKDAATSLKTGSVWNAGNIV 784 Query: 361 GPVIDQASFNKIMDYIEIGKEEGRLVSGGKGDDSKGYFIEPTIFADLDPKARLMQEEIFG 420 GP+I + +K++ + E LV + D + Y + PT+ + P++ + E+FG Sbjct: 785 GPMITNKN-DKLLQAFNLEPGESWLVPP-RFIDRREYILAPTVKWGVKPESFSFRTELFG 842 Query: 421 PVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIV 480 P+++ + + + +E + + N +YGLT + + + K GNLY NR TGAIV Sbjct: 843 PLLSVACIENLEEGIRLVNGLDYGLTSGLQSLDEKEQKLWKNSVMAGNLYINRGITGAIV 902 Query: 481 GYHPFGGFKMS--GTDSKAGGPDYLALHMQ 508 PFGG K+S G KAGGP+Y ++ Sbjct: 903 NRQPFGGMKLSAFGGGIKAGGPNYCTCFLE 932 Lambda K H 0.315 0.133 0.382 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: 1242 Number of extensions: 72 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: 516 Length of database: 1106 Length adjustment: 40 Effective length of query: 476 Effective length of database: 1066 Effective search space: 507416 Effective search space used: 507416 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 (21.6 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