Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 164 bits (414), Expect = 2e-44 Identities = 138/453 (30%), Positives = 205/453 (45%), Gaps = 15/453 (3%) Query: 33 SGETFECLSPVDGR-FLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFA 91 +G T + +P D R + S D A +A+ NA A + W +L A R A L A Sbjct: 592 AGATVQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHG--WDRLPAASRAAILEHAA 649 Query: 92 DLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD--EVAPTPHDQ 149 + L E L + GK + D+ + +I AA + + A + + E P P + Sbjct: 650 EQLEARRGEFIALCVREAGKGLPDAIA-EIREAADFLRYYATMARRYFGQPEQLPGPTGE 708 Query: 150 LGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIE 209 + GV I PWNFPL + ++ ALA GNSV+ KP+E++ L QL E Sbjct: 709 SNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHE 768 Query: 210 AGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQL--MVYAGESNMKRIWLE 267 AG+PA VL LPG G TVG AL V + FTGST+ A + + A + + + E Sbjct: 769 AGVPADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAE 828 Query: 268 AGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALK 327 GG++ I + A Q +A +SA + G+ C+A L V+ I DK M+ A+ Sbjct: 829 TGGQNAMIADSSALPEQIVKDAVSSAFQ-SAGQRCSAARVLYVQEDIADKVCAMLAGAMA 887 Query: 328 GWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTI 387 K G+P T VG ++D ++ + ++ K+ GT+ P Sbjct: 888 ELKVGDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKIGEVALDPATTGNGTFFAPRA 947 Query: 388 FDGVTNAMRIAQEEIFGPVLSVIAFDTAE--EAVAIANDTPYGLAAGIWTSDISKAHKTA 445 ++ + EIFGPVL VI + +E + V N T YGL GI + Sbjct: 948 YE--IPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQ 1005 Query: 446 RAVRAGSVWVNQYDGGDMTA--PFGGFKQSGNG 476 R G+ +VN+ G + PFGG SG G Sbjct: 1006 SRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTG 1038 Lambda K H 0.316 0.132 0.390 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: 1107 Number of extensions: 56 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: 497 Length of database: 1074 Length adjustment: 40 Effective length of query: 457 Effective length of database: 1034 Effective search space: 472538 Effective search space used: 472538 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: 55 (25.8 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