Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= curated2:Q2G9T9 (471 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 195 bits (496), Expect = 5e-54 Identities = 135/442 (30%), Positives = 214/442 (48%), Gaps = 14/442 (3%) Query: 6 IVSHEPATGAEV----WRGKVGDVEEVVARARRAWPAWAAQPLATRIELVRRFANEVRKD 61 I S PA AEV +G +V+ + A++A+PAW A R + R A+ R+ Sbjct: 534 IASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRR 593 Query: 62 ADNLATMISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAALRHKP 121 L+ E GK +A +V ++ ++ + R++ A L ++P Sbjct: 594 MFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQP 653 Query: 122 HGVLAVLGPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVV 181 G+ AV+ P+NFP + G A++ GN V+FKPS G L + F AG+P V Sbjct: 654 KGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVF 713 Query: 182 QVLIG-GPEEGQALVAHDGIDGVLFTGSAHAGIAINRKLAS-NPG----KIVALEMGGNN 235 + G G LV H + + FTGS G+ I K A PG K V EMGG N Sbjct: 714 NYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKN 773 Query: 236 PIVVWDTPKIEDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGA 295 I++ D +++A ++ SAF GQ+C+A R+I+ ++D ++ + + A I +G Sbjct: 774 AIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIG- 832 Query: 296 PFDDPAPFMGPVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAVA 355 P +DPA +MGPV D + E +V + G+ + + + ++ I++ Sbjct: 833 PSEDPANYMGPVADASLQKNILE-YVKVAEQEGKVLVKRTDIPAEGCYVPLTIVEGIKPH 891 Query: 356 DR-PDVELFGPLLQVVRVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVN 414 R E+FGP+L V+R +FDEA+A AN TRF L+ + P++ + R G + Sbjct: 892 HRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLY 951 Query: 415 WNRPTNGAS-SAAPFGGVGLSG 435 NR + GA PFGG +SG Sbjct: 952 LNRGSTGAMVERQPFGGFKMSG 973 Lambda K H 0.319 0.135 0.403 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: 1086 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: 471 Length of database: 1013 Length adjustment: 39 Effective length of query: 432 Effective length of database: 974 Effective search space: 420768 Effective search space used: 420768 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 (21.7 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