Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_011840207.1 RSPH17029_RS00810 aldehyde dehydrogenase family protein
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_000015985.1:WP_011840207.1 Length = 486 Score = 142 bits (358), Expect = 3e-38 Identities = 140/477 (29%), Positives = 215/477 (45%), Gaps = 37/477 (7%) Query: 87 NPASHGPVATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDV 146 +P++ A S D AA+ +A A + WA+TP A+R + + Sbjct: 26 DPSTEEACAVISLGDQADTDAAVAAAKAAFEGWAATPPAERLRLVKGILAQYEARKEEMA 85 Query: 147 MALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVH-HAPGVWNRVEYRPLE 205 A+++ G A A L +K E++ +P+ HAP +R+ P+ Sbjct: 86 QAISLE-MGAPIDLARNSQAPCLPWHLTNFLKAFEEIEWVRPLGPHAPN--DRIALEPI- 141 Query: 206 GFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQ 264 G V I+P+N+ L PAL+ G V KPS A S+ L + + +AGLP V Sbjct: 142 GVVGLITPWNWPMNQVTLKVIPALLAGCTCVLKPSEEAPLSSLLFAEFVHDAGLPAGVFN 201 Query: 265 FVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGK 324 V G+ V + HPD + FTGST G+ ++ AA S R+ E GGK Sbjct: 202 LVNGDGAGVGTQLSSHPDVEMISFTGSTRA-----GRAISKAAA---ESLKRVTLELGGK 253 Query: 325 NFHLIHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVG 384 +LI AD R A + V+ F GQ C+A +R+ V D +E A A +V Sbjct: 254 GANLIFADADER-AVERGVKHCFNNSGQSCNAPTRMLVERPFYDRAVEIAAEVAAKTRVA 312 Query: 385 PPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGG---SYDSSKGWYIQPTVYRT 441 + GPV+++ F ++ I + D L+AGG ++G++++PTV+ Sbjct: 313 SAHEEGPHIGPVVNKRQFEQIQSYIQKG-IDEGARLVAGGLGRPDGLNRGFFVRPTVFAD 371 Query: 442 TNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQD---REAL 498 P + E+FGP+L + P TE + RIA YGLT V ++D R L Sbjct: 372 VTPGMTIEREEIFGPVLSI--LPFETEEEAVRIANDT----PYGLTNYVQSEDGARRNRL 425 Query: 499 AVANDVLRNAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSI 555 A R +G +N KS GA PFGG +ASG + G + F+ +++I Sbjct: 426 A-----RRLRSGMVEMNGKSRGA---GAPFGGVKASGRAREGGVWG-IEEFLEVKAI 473 Lambda K H 0.316 0.130 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: 582 Number of extensions: 22 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: 572 Length of database: 486 Length adjustment: 35 Effective length of query: 537 Effective length of database: 451 Effective search space: 242187 Effective search space used: 242187 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