Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_043769867.1 U743_RS16355 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000733765.1:WP_043769867.1 Length = 494 Score = 238 bits (608), Expect = 3e-67 Identities = 156/479 (32%), Positives = 239/479 (49%), Gaps = 17/479 (3%) Query: 41 INGE-RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WRYTSPEER 97 I GE R E+ A+ +++ E V+G + +S ++A++AA KAF + W +P ER Sbjct: 20 IAGEWRDESGAERITVTDPASETVLGDIPCSSAATVDKAVRAARKAFNDPAWSNLAPMER 79 Query: 98 AAVLFRAAAKVRRRKHEFSALLVKEAGKPWN-EADADTAEAIDFMEYYARQMIELAKGKP 156 A+L R AA V + + + + + GKP + D + ++ Y+A +L+ Sbjct: 80 EALLHRLAALVEQHADDLATIESLDNGKPIAFSSTLDVPLSAQWLHYFAGWPSKLSGRSM 139 Query: 157 VNSREGEKNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVI 213 + + + + YT P GV I PWNF + + GNTVV+KPA TP Sbjct: 140 HPAVQPTGSHHAYTLRQPVGVVGAIVPWNFPLVLAIWKLAPALAAGNTVVIKPAEQTPYS 199 Query: 214 AAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKV 273 K E++E +G P GVVN V G G G +VDHP I+FTGS VG + AA Sbjct: 200 LLKLAELIEAAGFPPGVVNVVLGDGRTTGQAIVDHPGVDKISFTGSTAVGKHLLTSAA-- 257 Query: 274 QPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVY 333 LKRV E+GGK V+ DAD+E A + F +GQ C AG+R K + Sbjct: 258 ----NDLKRVTLELGGKSPTVILPDADLETAIPGAAQAVFVNSGQICFAGTRLFAPRKHF 313 Query: 334 DQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD 392 D++LE V E +S + +GPV+ Q D I+ +E G + G GG D Sbjct: 314 DRILEGVAEAAKSFPVGAGLDPNSMLGPVVSQQQMDSILGKVEAGVKAGASTFCGGGRLD 373 Query: 393 SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNN 452 +GYF++PTI D + +EEIFGPV+ + + D+ + +AN++EYGL+ + T++ Sbjct: 374 REGYFLEPTILVTDDAQNPAYREEIFGPVLTATRYDELDDIIAMANDSEYGLSANLYTSH 433 Query: 453 RKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 511 R + G ++ N + + PFGGFK SG + G D A + + K++ Sbjct: 434 FGLAHRLAAQLQAGTVWINTQLSPD--PHIPFGGFKQSGW-GRENGEDVFAHYTETKSV 489 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: 584 Number of extensions: 31 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: 494 Length adjustment: 34 Effective length of query: 481 Effective length of database: 460 Effective search space: 221260 Effective search space used: 221260 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 Sep 24 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