Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 242 bits (618), Expect = 2e-68 Identities = 158/462 (34%), Positives = 245/462 (53%), Gaps = 22/462 (4%) Query: 41 INGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WRYTSPEE 96 I+G+ V++ + I P D + V+ + + A+++A +AFE W +P + Sbjct: 22 IDGQYVDSLSGETFACIYPGDGRPLTD-VASCNAADVDVAVRSARRAFEAGVWSRMAPAD 80 Query: 97 RAAVLFRAAAKVRRRKHEFSALLVKEAGKPW-NEADADTAEAIDFMEYYARQMIELAKGK 155 R +L R + + + E + L GKP N + D A + +YA + I+ G+ Sbjct: 81 RRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVSAAACIAWYA-EAIDKVYGE 139 Query: 156 PVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAA 215 + + P G+ + PWN+ ++ A + TGN+V+LKPA +P A Sbjct: 140 VAATAHDMTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALATGNSVILKPAEQSPFTAL 199 Query: 216 KFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQP 275 KF E+ E+G+P GV+N VPG G G L H + FTGS EVG + + Sbjct: 200 KFGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFTGSTEVGKYFMQYS----- 254 Query: 276 GQQHLKRVIAEMGGKDTVVVDEDA-DIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYD 334 GQ ++KR+ E+GGK VV D D++ AA I F GQ C+AGSR +V EK++D Sbjct: 255 GQSNIKRIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCNAGSRLIVDEKIHD 314 Query: 335 QVLERVIEITESKVTAKPDSAD--VYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--T 389 Q+LE++ ++KV A D D MG ++ + D+++ YI+ G+ +G R V GG Sbjct: 315 QLLEKI--AAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRADGARPVIGGGRV 372 Query: 390 GDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVI 449 ++ G++I+PTIF + ++ QEEIFGPV++ V FDEA+ VAN+T YGL GAV Sbjct: 373 KTETGGFYIEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVANDTVYGLAGAVW 432 Query: 450 TNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 T + K+ RA + G ++ N G++ PFGGFK SG Sbjct: 433 TGSVKNAHRAAKSLRAGVVWVNCFDRGSLA--VPFGGFKQSG 472 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: 581 Number of extensions: 27 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: 515 Length of database: 495 Length adjustment: 34 Effective length of query: 481 Effective length of database: 461 Effective search space: 221741 Effective search space used: 221741 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 10 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