Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_900177295.1:WP_179243903.1 Length = 480 Score = 285 bits (728), Expect = 3e-81 Identities = 173/483 (35%), Positives = 264/483 (54%), Gaps = 18/483 (3%) Query: 40 VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99 +I GE V+ + NP+D +VVG ++ A QAI AAA AF W ++P++R Sbjct: 7 LIAGEWVDAPNASENRNPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQRFD 66 Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159 +L A ++ RK E LL +E GK E +T A +++A + + +A + ++ Sbjct: 67 ILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRIDST 126 Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219 R G + P GV +I PWNF AI A + GN VV+KPA P A + Sbjct: 127 RPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWALAD 186 Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279 +L+ +GLPKGV N V G G+ VG+ ++ PK + I+FTGS G + R + + Sbjct: 187 ILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIE----GEA 242 Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339 +K+ EMGGK+ VV +DAD+E+AA S AF GQ+C+A SR +V E ++D R Sbjct: 243 MKKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHD----R 298 Query: 340 VIEITESKVTA-KPDSA---DVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDD 392 +E SK+ A K D+A +GPV+DQ D+ + YI++G+ EG +L GG + Sbjct: 299 FVEALTSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRE 358 Query: 393 SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNN 452 ++G++++P +F + D R+ +EEIFGPV + +V D+D AL VAN+T++GL+ + T++ Sbjct: 359 TEGFYLQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSS 418 Query: 453 RKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKTI 511 KH E K+ G + N G V YH PFGG K S ++ G + + KT Sbjct: 419 LKHAEHFKRNSQAGMVMVNLPTAG--VDYHVPFGGRKNSSYGAREQGRYAVEFYTTVKTA 476 Query: 512 SEM 514 M Sbjct: 477 YAM 479 Lambda K H 0.316 0.133 0.379 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: 568 Number of extensions: 27 Number of successful extensions: 4 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: 515 Length of database: 480 Length adjustment: 34 Effective length of query: 481 Effective length of database: 446 Effective search space: 214526 Effective search space used: 214526 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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