Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_084610117.1 A3GO_RS0114220 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::ANA3:7023590 (1064 letters) >NCBI__GCF_000428045.1:WP_084610117.1 Length = 1032 Score = 1240 bits (3208), Expect = 0.0 Identities = 637/1031 (61%), Positives = 781/1031 (75%), Gaps = 4/1031 (0%) Query: 33 YIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQQYSLET 92 Y VDE L LI L + E +++ TR + ELV VR D M IDA L +YSL+T Sbjct: 2 YCVDESSLLETLIPLARPTPELLKKTTRESAELVRAVRARDDAMHM--IDALLLEYSLDT 59 Query: 93 QEGIILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGLMLTGKI 152 +EG++LMCLAE+L+RIPD+ATADALI+DKL A W +HL +S S+LVNASTWGL+LTGK+ Sbjct: 60 REGVLLMCLAESLMRIPDSATADALIKDKLGIADWKQHLKQSKSLLVNASTWGLLLTGKV 119 Query: 153 VKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKNSEDKRK 212 + LD I+ P+++++RLVNRL EPV+RQAM AMKIMG+QFVLGRT+ EAL NS +R+ Sbjct: 120 ITLDAGIEDEPASVINRLVNRLSEPVVRQAMHQAMKIMGRQFVLGRTITEALANSRKQRE 179 Query: 213 LGYTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTISIKLSALHPRY 272 GY++SYDMLGEAALT +DAE YF Y+ AI +G+ ++ + S R T+SIKLSALHPRY Sbjct: 180 AGYSYSYDMLGEAALTDRDAEHYFEAYSGAIKAIGSDTFPSDTSFRSTVSIKLSALHPRY 239 Query: 273 EVANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWG 332 E E RV++EL D ++ LIKLAR L++GI+IDAEE DRLELSLKLF++L+ ++GWG Sbjct: 240 EQQQERRVISELGDRMLALIKLARELDVGITIDAEEADRLELSLKLFERLYRDQISRGWG 299 Query: 333 LLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYT 392 LG+VVQAY KRALPVL WL LA +QGD IP+RL KGAYWDSE+K AQQ G +YP++T Sbjct: 300 NLGLVVQAYQKRALPVLFWLAALAGKQGDLIPLRLAKGAYWDSEIKHAQQLGLESYPVFT 359 Query: 393 RKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQRLHGMGQE 452 RK TDVSYLACA +LLSD +G IYPQFASHNA TVA++ MA +EFQRLHGMG Sbjct: 360 RKEATDVSYLACASFLLSDQLKGLIYPQFASHNAHTVASVVSMATHDQYEFQRLHGMGDA 419 Query: 453 LYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVVH 512 LY+ ++ E A VRIYAP+G+HKDLLPYLVRRLLENGAN+SFVH+L+D KTP+ESL+ H Sbjct: 420 LYEAVI-ERYASRVRIYAPVGSHKDLLPYLVRRLLENGANSSFVHRLIDQKTPVESLIEH 478 Query: 513 PLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAGP 572 PL L Y +L+N +I LP DI+G R NS G+N+N+ + P + F W A P Sbjct: 479 PLTKLCQYSSLSNERIPLPPDIYGKGRINSCGVNINVADQWLPLQREVQAFFRQSWHAAP 538 Query: 573 LVNGQTL-TGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRAS 631 L+ G+ + +GE V +P D VG + D+ + QA+A A AFA W TPV R+ Sbjct: 539 LIKGKRIESGEVVQVHAPHDRVIHVGSLIQTDEQTVGQAIAVACEAFAGWNATPVAKRSV 598 Query: 632 ALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLP 691 AL++ ADLLEE+R ELIALC EAGK+IQD IDEVREAVDFCRYYA QA+ +LL Sbjct: 599 ALERAADLLEEHRAELIALCHLEAGKTIQDAIDEVREAVDFCRYYAWQARLHFDSAQLLD 658 Query: 692 GPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAV 751 GPTGE NEL+LQGRG+FVCISPWNFPLAIF GQV AALAAGN+V+AKPAEQTS+I RAV Sbjct: 659 GPTGEANELYLQGRGLFVCISPWNFPLAIFTGQVMAALAAGNSVIAKPAEQTSLIAARAV 718 Query: 752 QLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAII 811 +L HQAGIP VL LPG G+ +G LTADERI GV FTGST TA+LINR+LA R G + Sbjct: 719 ELFHQAGIPDSVLHLLPGEGSRIGPLLTADERIAGVAFTGSTETARLINRSLAMRNGPVA 778 Query: 812 PLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQ 871 L+AETGGQNAMVVDST+ PEQV+ DV+SS+F SAGQRCSALRVLFLQ+D+A+R++ +L+ Sbjct: 779 TLVAETGGQNAMVVDSTALPEQVIKDVISSAFASAGQRCSALRVLFLQDDVAERILALLK 838 Query: 872 GAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMSLPAGTENGHFVS 931 GAM EL +G+P + TDVGPVID A+ L HI +++ LI + LP E G FV+ Sbjct: 839 GAMAELKVGDPCELDTDVGPVIDEEARRTLQRHIAEMREQATLIAETPLPLNAEAGCFVA 898 Query: 932 PTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHALEV 991 P A EI + L KEHFGP+LHVIR+KAS L VI +IN++G+GLTLGIHSRNE + + Sbjct: 899 PVAFEIQHMDQLSKEHFGPVLHVIRFKASRLDDVILQINNSGYGLTLGIHSRNETTSRYI 958 Query: 992 ADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIG 1051 +V VGNVYINRNQIGAVVGVQPFGG GLSGTGPKAGGPHYL RF TE+TRT N TAIG Sbjct: 959 DTRVRVGNVYINRNQIGAVVGVQPFGGLGLSGTGPKAGGPHYLLRFATERTRTTNTTAIG 1018 Query: 1052 GNATLLSLGDS 1062 GNATLLSL +S Sbjct: 1019 GNATLLSLENS 1029 Lambda K H 0.317 0.133 0.377 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: 2422 Number of extensions: 91 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: 1064 Length of database: 1032 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 987 Effective search space: 1005753 Effective search space used: 1005753 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: 58 (26.9 bits)
This GapMind analysis is from Sep 24 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