Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 229 bits (585), Expect = 3e-64 Identities = 151/468 (32%), Positives = 230/468 (49%), Gaps = 15/468 (3%) Query: 14 FIDGAWVDADNGQTIKVNNPAT-GEILGTVPKMGAAETRRAIEAADKALPAWRALTAKER 72 FI G V D+ TI NPA E++ V + G E AIEAA KA PAWR + +R Sbjct: 522 FIGGKDVTTDD--TIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADR 579 Query: 73 ATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIP 132 A L R ++ +L+ LE GK +A ++ F++++A E R+ Sbjct: 580 AMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRM 639 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192 G P + + QP G+ A I PWNFP A+ A A+ G ++ KP+S + L Sbjct: 640 GRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNL 699 Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK----- 247 E+ + AG+P GVF+ V G + +G L +P V + FTGS E+G ++ + AK Sbjct: 700 TEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQ 759 Query: 248 -DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFA 306 K+V E+GG I+ DDADLD+AV + S + GQ C +R+ + D +YD F Sbjct: 760 MQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFV 819 Query: 307 EKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGK-PMEGNF 365 E+L A +KIG + GP+ D + E++ A +G ++ P EG + Sbjct: 820 ERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCY 879 Query: 366 FEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVF 425 TI+ + + +A+EE FGP+ + R + + +A++N T F L ++R + Sbjct: 880 VPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLT 939 Query: 426 RVAEALEYGMVGVNTGLISN--EVAPFGGIKASGLGREGSKYGIEDYL 471 + G + +N G E PFGG K SG+ GSK G DYL Sbjct: 940 KARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGV---GSKTGGPDYL 984 Lambda K H 0.317 0.135 0.390 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: 54 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: 480 Length of database: 1013 Length adjustment: 39 Effective length of query: 441 Effective length of database: 974 Effective search space: 429534 Effective search space used: 429534 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