Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 209 bits (531), Expect = 2e-58 Identities = 155/475 (32%), Positives = 234/475 (49%), Gaps = 36/475 (7%) Query: 32 YLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRY 91 ++G + ++GE + I+P D + V +V++ E A+ AA KAF W Sbjct: 25 FIGGKFVPPVDGEYFDV------ISPVDGQ-VFTKVARGKAADIELALDAAHKAFPAWSR 77 Query: 92 TSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQMIE 150 TS ER+ +L + A ++ + +A+ + GKP E +AD A +D Y+A +I Sbjct: 78 TSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAG-VIR 136 Query: 151 LAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVLKPASA 209 +G + + V P G+ I PWNF +MA +AP + G ++KPA Sbjct: 137 AEEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPM-LMATWKMAPALAAGCCTIVKPAEQ 195 Query: 210 TPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFER 269 TP +EV+ + LP GV+N V G G E G L P+ + FTG G I + Sbjct: 196 TPASIMILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQY 254 Query: 270 AAKVQPGQQHLKRVIAEMGGKDTVVVDE---DADIELAAQSIFTSAFGFA---GQKCSAG 323 A+ ++L V E+GGK V DAD E + + A FA G+ C+ Sbjct: 255 AS------ENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCL-EGAVMFALNQGEVCTCP 307 Query: 324 SRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGR 383 SR +VHEK+YD +E+VI E+ P MG + ++KI+SYI+IGKQEG Sbjct: 308 SRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGA 367 Query: 384 LVSGGTGDDSK-------GYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEV 436 V G G+ +K GY++KPT+ + K R+ QEEIFGPV + D +EA+ + Sbjct: 368 EVLTG-GEVAKLNSGLENGYYVKPTLLKGHN-KMRVFQEEIFGPVCSVATFKDVEEAISI 425 Query: 437 ANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 +N+T YGL V T + + + G ++ NC A + PFGG+K SG Sbjct: 426 SNDTLYGLGAGVWTRDAHEAYQVPRAIKAGRVWV--NCYHAYPAHAPFGGYKKSG 478 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: 602 Number of extensions: 37 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: 509 Length adjustment: 35 Effective length of query: 480 Effective length of database: 474 Effective search space: 227520 Effective search space used: 227520 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