Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_089216122.1 CHB69_RS10610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::ANA3:7023590 (1064 letters) >NCBI__GCF_900188185.1:WP_089216122.1 Length = 1030 Score = 907 bits (2345), Expect = 0.0 Identities = 498/1030 (48%), Positives = 677/1030 (65%), Gaps = 26/1030 (2%) Query: 37 EEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGI 96 E +++L + S E VT R L+ K + ++ +V + +Y L T+EG+ Sbjct: 18 EADIVADLRTALARSPATAEAVTARGLTLIRKAKAEGERETLVA--QLMNRYRLSTEEGV 75 Query: 97 ILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLD 156 +LMCLAEALLR+PD ATA+ALI DK++G W E + ++V S GL L + LD Sbjct: 76 VLMCLAEALLRVPDNATANALIRDKIAGRHWAEGDDEDSPLVVALSARGLSLGSATLMLD 135 Query: 157 KK-IDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKNSE-DKRKLG 214 P +L ++ R GEPVIRQA +AAMK++G+QFV+G ++ A++ ++ DK +L Sbjct: 136 AMGSQAKPLAILRTMIRRSGEPVIRQAALAAMKLLGQQFVMGESIDAAVRRADKDKSELA 195 Query: 215 YTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTISIKLSALHPRYEV 274 S+DMLGEAA T DA +Y++ YA AI +G + + ISIKLSALHPRYE Sbjct: 196 ---SFDMLGEAARTAADARRYYDSYAAAIARIGRDAKPGDPFANHGISIKLSALHPRYEY 252 Query: 275 ANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWGLL 334 RV EL VI L AR +NI + IDAEE DRLE L ++ L +A GW L Sbjct: 253 LQGQRVRDELIPRVIELAVAARRVNIPLMIDAEESDRLEPHLDVYGALIDAGIADGWTGL 312 Query: 335 GIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRK 394 GIVVQAY KRA V+ W+ A+ +G + +RLVKGAYWD+E+K AQ G +P++T K Sbjct: 313 GIVVQAYQKRASEVIRWVAARARRRGVMLSMRLVKGAYWDTEIKRAQTLGLGDFPVFTAK 372 Query: 395 AGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQRLHGMGQELY 454 TD++YLACA+ L + I+P FASHNA T+A ++++ ++E QRLHGMG+ + Sbjct: 373 LHTDLNYLACAQILRE--CQDCIFPAFASHNAMTLAFVTELFAGADYELQRLHGMGEGAH 430 Query: 455 DTILS-EAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVVHP 513 D I++ + VR+YAP+G H+DLL YLVRRLLENGAN+SFVH+ DP E L V P Sbjct: 431 DAIVALSPPPRPVRVYAPVGTHRDLLAYLVRRLLENGANSSFVHQFSDPDVSAEELAVDP 490 Query: 514 LKTLTGYKTLANNKIVLPT--DIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAG 571 +++A+ LPT ++ R+NS+G ++ E AA+ + + A Sbjct: 491 -------RSVASAPSKLPTGLQLYDPVRRNSRGYDLGEPGVPEALIAAIAEARDAGAVAA 543 Query: 572 PLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRAS 631 P+V G+ G+ + V +P T +G+V AD AA+E+AVA+A A W+ RA Sbjct: 544 PIVGGRERRGKGEPVHNPA-TGVVIGRVVEADAAAVEEAVAAARKAQGDWSLAGGAFRAE 602 Query: 632 ALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLP 691 L++ ADL+EE + L EAGK++ D + EVREAVDF RYYA QA+ S P LP Sbjct: 603 RLERAADLIEERDALFLGLAMDEAGKTLVDAVAEVREAVDFLRYYAAQARADFSWPVTLP 662 Query: 692 GPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAV 751 GPTGE NEL L+G+G+F CISPWNFPLAIFLGQVSAALAAGN V+AKPAEQT +I + AV Sbjct: 663 GPTGERNELILEGKGIFACISPWNFPLAIFLGQVSAALAAGNAVLAKPAEQTPLIAHAAV 722 Query: 752 QLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAII 811 + +AG+P D+L YLPG G TVG ALT + + GV FTGST A+ INR+LA REG I Sbjct: 723 ETLLEAGVPGDILHYLPGRGETVGAALTGHDDVIGVAFTGSTEVARAINRSLAMREGPIA 782 Query: 812 PLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQ 871 LIAETGG NAM+VDST+ PEQV D V+S+F SAGQRCSALR+L +Q+D+AD +I ++ Sbjct: 783 TLIAETGGANAMIVDSTALPEQVARDAVASAFQSAGQRCSALRLLCVQDDVADAMIAMVA 842 Query: 872 GAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMS---LPAGTENGH 928 GAM EL +G+P+ + TDVGP+ID A++N+ A+++ + G+LI + + LPAG G Sbjct: 843 GAMAELNVGDPAILATDVGPIIDEEAQSNIAAYVEEARAAGRLIAEAARTKLPAG---GT 899 Query: 929 FVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHA 988 FV+P + +D + L++E FGP+LHV +K EL +ID IN++G+GLTLG+H+R + A Sbjct: 900 FVAPAMIRLDHVTDLKREIFGPVLHVATWKGGELDALIDAINASGYGLTLGVHTRIDSVA 959 Query: 989 LEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNIT 1048 VA + VGNVY+NRNQIGA+VG QPFGG+GLSGTGPKAGGP+YL RF EK+ + +IT Sbjct: 960 AHVAARAQVGNVYVNRNQIGAIVGSQPFGGRGLSGTGPKAGGPNYLRRFAEEKSISTDIT 1019 Query: 1049 AIGGNATLLS 1058 A GGNA L++ Sbjct: 1020 AAGGNAALMA 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: 2394 Number of extensions: 98 Number of successful extensions: 7 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: 1030 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 985 Effective search space: 1003715 Effective search space used: 1003715 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