Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__MR1:202865 Length = 1059 Score = 190 bits (483), Expect = 2e-52 Identities = 153/471 (32%), Positives = 234/471 (49%), Gaps = 37/471 (7%) Query: 2 THWIAGEWVQGQ---GEEFVSLSPYNQ-EVIWRGNGATAEQVDQAVAAARAAFVEWKKRP 57 T W AG V GQ GE +SP++ + + + A ++QAV++A AAF W + P Sbjct: 561 TQWQAGPLVNGQPLTGEHKTIVSPFDTTQTVGQVAFADKAAIEQAVSSAHAAFGSWTRTP 620 Query: 58 FAEREAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEA----------AAMAGKIAI 107 R + + A+ ++EN E++ + +E GK I + E A A K+ Sbjct: 621 VEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMS 680 Query: 108 SIRAYHDRTGEATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVF 167 TGE N++ L+ R GV P+NFP + G + AL AGNTVV Sbjct: 681 KPELLPGPTGEL------NELFLQGR--GVFVCISPWNFPLAIFLGQVSAALAAGNTVVA 732 Query: 168 KPSEQTPWTGELAMKLWEEAGLPKGVINLVQGAKET-GIALADAKGIDGILFTGSANTGH 226 KP+EQT G A++L +AG+P V+ + G T G AL + I G+ FTGS T Sbjct: 733 KPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAK 792 Query: 227 ILHRQFAGQPGKMLAL--EMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRL 284 +++R A + G ++ L E GG N MV+ D+ + V ++ S+F SAGQRC+ R L Sbjct: 793 LINRTLANREGAIIPLIAETGGQNAMVV-DSTSQPEQVVNDVVSSSFTSAGQRCSALRVL 851 Query: 285 YVPFGEKGDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQAN----LQS 340 ++ + D +I L A + + P + +GP I A AK LDA + + Sbjct: 852 FLQ-EDIADRVIDVLQGAMDELVIGNPSSIKTD-VGPVID-ATAKANLDAHIDHIKQVGK 908 Query: 341 LGGESLIEAKAGEAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLDKA--VELANDT 398 L + + A FV+P +++ +I L ++E+FGP+L V+RY+ + A ++ N T Sbjct: 909 LIKQMSLPAGTENGHFVAPTAVEIDSIKVL-EKEHFGPILHVIRYKASELAHVIDEINST 967 Query: 399 RFGLSAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGA-SGDAPFGGPGASG 448 FGL+ G+ S ++ D + G V NR GA G PFGG G SG Sbjct: 968 GFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1018 Lambda K H 0.316 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: 1110 Number of extensions: 55 Number of successful extensions: 6 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: 485 Length of database: 1059 Length adjustment: 39 Effective length of query: 446 Effective length of database: 1020 Effective search space: 454920 Effective search space used: 454920 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