Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 207 bits (528), Expect = 6e-58 Identities = 153/479 (31%), Positives = 236/479 (49%), Gaps = 34/479 (7%) Query: 27 ATVSEYLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAF 86 A ++G + + GE + +++P D + V + +++ E A+ AA A Sbjct: 17 ARYDNFIGGKWVPPVGGEYFD------NVSPVDGK-VFCQAARSDYRDIELALDAAHAAK 69 Query: 87 EEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYA 145 + W TS ER+ +L + A +V + + + E GK E +AD +D Y+A Sbjct: 70 DSWGKTSVTERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFA 129 Query: 146 RQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVL 204 I +G + + ++ P GV I PWNF +MA +AP + GN VVL Sbjct: 130 G-CIRAQEGSAADLDANTVSYHLPEPLGVVGQIIPWNFPL-LMAAWKIAPALAAGNCVVL 187 Query: 205 KPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGT 264 KPA TP +E +E+ LP GV+N V G GAE G L + + + FTGS EVG Sbjct: 188 KPAEQTPASIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGN 246 Query: 265 RIFERAAKVQPGQQHLKRVIAEMGGKDT------VVVDEDADIELAAQSIFTSAFGFAGQ 318 I + AA ++L E+GGK V+ ED ++ A + + + F G+ Sbjct: 247 HILKCAA------ENLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLAFFN-QGE 299 Query: 319 KCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIG 378 C+ SR +V E +YD +E+VI ++ P D +G + YDKI+ Y++IG Sbjct: 300 VCTCPSRVLVQESIYDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIG 359 Query: 379 KQEG-RLVSGG-----TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDE 432 + EG +++ GG G + GY+I+PTI + K R+ QEEIFGPVV+ D E Sbjct: 360 RAEGAKVLMGGEFKLQDGPEKGGYYIQPTILKGHN-KMRVFQEEIFGPVVSVTTFKDEAE 418 Query: 433 ALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 AL +AN+T+YGL V T + +R + G ++ NC A + FGG+K SG Sbjct: 419 ALAIANDTQYGLGAGVWTRDMNLAQRMGRGIQAGRVWI--NCYHAYPAHAAFGGYKKSG 475 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: 612 Number of extensions: 33 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: 515 Length of database: 506 Length adjustment: 35 Effective length of query: 480 Effective length of database: 471 Effective search space: 226080 Effective search space used: 226080 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 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