Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_086510760.1 BZY95_RS15250 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::ANA3:7023590 (1064 letters) >NCBI__GCF_002151265.1:WP_086510760.1 Length = 1063 Score = 1240 bits (3209), Expect = 0.0 Identities = 631/1064 (59%), Positives = 797/1064 (74%), Gaps = 10/1064 (0%) Query: 6 MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65 M A +L +LD LF ++++Y+VDEE ++ EL+ ++ ++ E R+ + EL Sbjct: 1 MLNAETMLDAATWQQDLDSLFSRISEHYVVDEETFVKELVNVLSANPEDFRRIADKTAEL 60 Query: 66 VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125 V +VR D + ID LQQYSL+T EG++LMCLAEA+LRIPD ATADALIEDKL A Sbjct: 61 VREVRDMDTA--VDTIDQLLQQYSLDTHEGLMLMCLAEAMLRIPDTATADALIEDKLGPA 118 Query: 126 KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185 W H+ +SDS LVNASTWGL++TG +V LDK DG PS ++RLVNR+GEPVIR+AM Sbjct: 119 DWKAHVGQSDSWLVNASTWGLLMTGHVVTLDKPRDGKPSGFINRLVNRMGEPVIRRAMYE 178 Query: 186 AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245 AMKIMGKQFVLGR + EALK S GYT+SYDMLGEAA TR DA++YF+DYA AI + Sbjct: 179 AMKIMGKQFVLGRDIDEALKRSRPLFDKGYTYSYDMLGEAARTRADAKRYFDDYAKAIRQ 238 Query: 246 LGAQSYNENE-SPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISI 304 +G S E +P P++SIKLSALHPRYE +++L EL +V L+ +AR ++ ++I Sbjct: 239 VGLTSTKLTERTPAPSVSIKLSALHPRYEFGRREQILHELVGSVRELVTMARERDVALTI 298 Query: 305 DAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIP 364 DAEEVDRLELSL++F+ ++ ++A KGWG G+VVQAYSKRALPVL +L RLA QGDEIP Sbjct: 299 DAEEVDRLELSLEVFRAVYESEACKGWGHFGLVVQAYSKRALPVLHYLNRLADRQGDEIP 358 Query: 365 VRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASH 424 VRLVKGAYWDSE+K +QQ G YP+YTRKA TDV+YL CAR+LLSD TRG I+PQFA+H Sbjct: 359 VRLVKGAYWDSEIKESQQLGVEGYPVYTRKACTDVAYLVCARFLLSDQTRGRIFPQFATH 418 Query: 425 NAQTVAAISDMAGD--RNHEFQRLHGMGQELYDTILSEAGAKAV-RIYAPIGAHKDLLPY 481 NA T++ I +MA + R EFQRLHGMG+ LYD L A RIYAP+GAHKDLLPY Sbjct: 419 NAHTISTILEMADEATRPFEFQRLHGMGEALYDAALKRAPKGTYCRIYAPVGAHKDLLPY 478 Query: 482 LVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKN 541 LVRRLLENGAN+SFVH+LVDPK P+E+L VHP++TL Y+T +N +I LP DI+G R+N Sbjct: 479 LVRRLLENGANSSFVHQLVDPKVPVETLCVHPVETLGQYRTFSNPRIPLPKDIYGERRRN 538 Query: 542 SKGLNMNIISEAEPFFAALDKFKSTQWQAGPLV--NGQTLTGEHKTVVSPFDTTQTVGQV 599 S+G+N+N+ S EP A+ F ++ GPL+ + + + G V SP+D Q VG V Sbjct: 539 SRGVNLNVRSHYEPLMKAMSGFMERSYEVGPLLAFDVERIAGNVHEVFSPYDRRQRVGSV 598 Query: 600 AFADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSI 659 + + +AV +A AAF W TPV RA+ +++L DL+EEN EL+ LC+RE GK + Sbjct: 599 QWTTRDQAARAVDAAWAAFPRWEATPVAERAAIIRRLGDLMEENLAELMTLCSREGGKLL 658 Query: 660 QDGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLA 719 DG+DE+REAVDFCRYYA++A++ +P LPGPTGE N L L G+GVF ISPWNFP+A Sbjct: 659 TDGVDEIREAVDFCRYYAMRAEEQFGEPLELPGPTGESNRLMLSGKGVFAAISPWNFPVA 718 Query: 720 IFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALT 779 IF GQV AA AGN+V+AKPAEQTSI+ +R ++L H+AG+P DV+Q LPG G TVG+ LT Sbjct: 719 IFCGQVVAAAVAGNSVLAKPAEQTSIVAHRVIELLHEAGMPRDVVQLLPGDGPTVGSVLT 778 Query: 780 ADERIGGVCFTGSTGTAKLINRTLANREGAIIP-LIAETGGQNAMVVDSTSQPEQVVNDV 838 +D RI GV FTG T TA++INR LA RE A +P L+AETGG NA++VDST+ PEQVV DV Sbjct: 779 SDPRITGVAFTGGTDTAQIINRALAARENAPLPALVAETGGMNALIVDSTALPEQVVADV 838 Query: 839 VSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAK 898 + S++ SAGQRCSALRVL+LQED+ADRVI++L+GAMDEL +G+P + TDVGPVID A+ Sbjct: 839 IQSAYQSAGQRCSALRVLYLQEDVADRVIEILRGAMDELHVGDPRDLGTDVGPVIDEDAR 898 Query: 899 ANLDAHIDHIKQVGKLIKQMSL-PAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRY 957 NL AHI+ +K G+L+ + L PA T +G FV P A ID+I LE+E FGP+LHV+RY Sbjct: 899 KNLLAHIEKLKGEGRLLAETRLDPAHTAHGTFVPPVAFSIDAIDALEREQFGPVLHVVRY 958 Query: 958 KASELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFG 1017 KASE+ V+D IN+ G+GLT G+HSRNE A VA K+ VGNVYINRN IGAVVGVQPFG Sbjct: 959 KASEIEQVLDSINARGYGLTFGVHSRNESFAQLVAQKIRVGNVYINRNIIGAVVGVQPFG 1018 Query: 1018 GQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1061 GQGLSGTGPKAGGPHYL RF TEKT T N A+GGNA+LL+LGD Sbjct: 1019 GQGLSGTGPKAGGPHYLLRFATEKTVTVNTAALGGNASLLALGD 1062 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: 2635 Number of extensions: 95 Number of successful extensions: 8 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: 1063 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 1018 Effective search space: 1037342 Effective search space used: 1037342 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