Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::ANA3:7023590 (1064 letters) >FitnessBrowser__PV4:5208103 Length = 1059 Score = 1848 bits (4786), Expect = 0.0 Identities = 923/1058 (87%), Positives = 996/1058 (94%) Query: 6 MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65 MFKASEVL GRYDSA LDELF A+T+NYIVDEEQYLSELIKLVPSSD+ I+R+T+RAH+L Sbjct: 1 MFKASEVLTGRYDSATLDELFTAITNNYIVDEEQYLSELIKLVPSSDDEIQRITKRAHDL 60 Query: 66 VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125 V+KVRQ+DKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALI+DKLSGA Sbjct: 61 VHKVRQYDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIDDKLSGA 120 Query: 126 KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185 KWDEHLSKSDS LVNASTWGLMLTGKI+ LDK IDG PS+LL+RLVNRLGEPVIRQAM+A Sbjct: 121 KWDEHLSKSDSTLVNASTWGLMLTGKIISLDKSIDGKPSSLLNRLVNRLGEPVIRQAMLA 180 Query: 186 AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245 AMKIMGKQFVLGRT++EALKNS DKRKLGYTHSYDMLGEAALT KDA+KY+ DY+NAI Sbjct: 181 AMKIMGKQFVLGRTVQEALKNSTDKRKLGYTHSYDMLGEAALTMKDAQKYYQDYSNAIAA 240 Query: 246 LGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 305 LGAQ Y+E+E+PRPTISIKLSALHPRYEVANEDR +TELYDT+I+L+ AR LN+G+SID Sbjct: 241 LGAQQYDESEAPRPTISIKLSALHPRYEVANEDRTMTELYDTLIKLVSQARSLNVGVSID 300 Query: 306 AEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 365 AEEVDRLELSLKLFQKL+N+DA KGWGLLG+VVQAYSKRALPVL W+TRLAK+QGDEIPV Sbjct: 301 AEEVDRLELSLKLFQKLYNSDAAKGWGLLGLVVQAYSKRALPVLCWITRLAKDQGDEIPV 360 Query: 366 RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 425 RLVKGAYWDSELKWAQ AGE YPL+TRKAGTDVSYLACARYLLSDATRGAIYPQFASHN Sbjct: 361 RLVKGAYWDSELKWAQVAGEGGYPLFTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 420 Query: 426 AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 485 AQTVAAI+DMAGDR +EFQRLHGMG+ELYDT+L+E+G VRIYAP+GAHKDLLPYLVRR Sbjct: 421 AQTVAAITDMAGDRLYEFQRLHGMGEELYDTLLAESGVSTVRIYAPVGAHKDLLPYLVRR 480 Query: 486 LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGL 545 LLENGANTSFVHKLVDPKTPIESLVVHPL TL YKTLANNKIV P DIFG++RKNSKG+ Sbjct: 481 LLENGANTSFVHKLVDPKTPIESLVVHPLTTLQSYKTLANNKIVQPIDIFGAERKNSKGI 540 Query: 546 NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKA 605 NMNIISE+EPFFAALDKFK QW AGP+VNG+TL+GE V SP+DTTQ VG+VAFA+ Sbjct: 541 NMNIISESEPFFAALDKFKDQQWSAGPIVNGETLSGETIEVKSPYDTTQIVGKVAFANNQ 600 Query: 606 AIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE 665 AIEQA+ASA AF +W TPVEVRA+ALQKLADLLEENREELIALCTREAGKSIQDGIDE Sbjct: 601 AIEQALASAHNAFGSWCSTPVEVRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660 Query: 666 VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 725 VREAVDFCRYYAVQAKK+M KPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV Sbjct: 661 VREAVDFCRYYAVQAKKMMGKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720 Query: 726 SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG 785 +AALAAGNTVVAKPAEQTSI+GYRAVQLAH+AGIP + LQ+LPGTGATVG +TADERIG Sbjct: 721 TAALAAGNTVVAKPAEQTSIVGYRAVQLAHEAGIPKEALQFLPGTGATVGATITADERIG 780 Query: 786 GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 845 GVCFTGST TAK IN TLA R+GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS Sbjct: 781 GVCFTGSTVTAKRINLTLAQRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 840 Query: 846 AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHI 905 AGQRCSALRVL+LQEDIADRVIDV++GAMDEL IGNP SVKTDVGPVIDATAKANL+AHI Sbjct: 841 AGQRCSALRVLYLQEDIADRVIDVMKGAMDELTIGNPGSVKTDVGPVIDATAKANLNAHI 900 Query: 906 DHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV 965 DHIKQVG+LI Q+ LPAGTENGHFV+PTAVEIDSIKVLEKEHFGPILHVIRYKA++L V Sbjct: 901 DHIKQVGRLINQLELPAGTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKAADLPKV 960 Query: 966 IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1025 ID+INSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG Sbjct: 961 IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020 Query: 1026 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSD 1063 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDS+ Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSE 1058 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: 3020 Number of extensions: 101 Number of successful extensions: 1 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: 1059 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 1014 Effective search space: 1033266 Effective search space used: 1033266 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 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