Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085640383.1 MGEO_RS16525 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::Phaeo:GFF1160 (1158 letters) >NCBI__GCF_002115805.1:WP_085640383.1 Length = 1140 Score = 1503 bits (3892), Expect = 0.0 Identities = 788/1137 (69%), Positives = 890/1137 (78%), Gaps = 11/1137 (0%) Query: 24 LRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAE 83 LR ID TY D+A D L A A L TDR I A A LV +IR S PGLMEVFL+E Sbjct: 9 LRPLIDDNTYADEALKVDSLRATAQLTQTDRDAIKARATKLVTEIREDSRPGLMEVFLSE 68 Query: 84 YGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALM 143 YGLST+EG+ALMCLAEALLRVPDA TIDALIEDKIAPS W HLG+STS LVNASTWALM Sbjct: 69 YGLSTEEGIALMCLAEALLRVPDAATIDALIEDKIAPSNWASHLGESTSPLVNASTWALM 128 Query: 144 LTGKVL-DEKRSPVSALRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGM 202 LTGKVL DE+ PV LRGA+KRLGEPVIRTAV RAMKEMG QFVLGETI+ AMKRAA M Sbjct: 129 LTGKVLKDEQPGPVGHLRGAIKRLGEPVIRTAVGRAMKEMGAQFVLGETIQSAMKRAARM 188 Query: 203 EAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHP 262 EAKGYTYSYDMLGEAARTE DA RYHL+YSRAISAIA A S DIR NPGISVKLSALHP Sbjct: 189 EAKGYTYSYDMLGEAARTETDARRYHLSYSRAISAIAEAAKSKDIRDNPGISVKLSALHP 248 Query: 263 RYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAG 322 RYE AQ+ +V ++VPRL+ LA LA++AG+GLN+DAEEADRLS+SL+VIE V+S+P+L G Sbjct: 249 RYEEAQQDTVMNEVVPRLRTLAQLARSAGIGLNIDAEEADRLSVSLDVIETVLSEPSLKG 308 Query: 323 WDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPV 382 WDGFGVVVQAYGPR G +D LY++A R DR++MVRLVKGAYWDTE+KRAQV G+ FPV Sbjct: 309 WDGFGVVVQAYGPRAGHVIDWLYNLAERLDRKIMVRLVKGAYWDTEIKRAQVAGLPAFPV 368 Query: 383 FTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGM 442 FT K TD+SYIANARKLL +TDRIYPQFATHNAHTV+AILHMA+D + +EFQRLHGM Sbjct: 369 FTAKHHTDISYIANARKLLGMTDRIYPQFATHNAHTVAAILHMAED--RTLFEFQRLHGM 426 Query: 443 GETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVA 502 GE LH++V + T CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVD +VP VA Sbjct: 427 GEALHDIVKDDEGTRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDTDVPAAEVA 486 Query: 503 ADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLL 562 ADPF L GP+LF PERPNS G+DL H PT AAI+AAR P+ W A PL+ Sbjct: 487 ADPFDT--QAVPKLPTGPELFAPERPNSKGWDLTHRPTRAAIEAARKPFSGVQWTATPLV 544 Query: 563 AKAPETATTTDEPVRNPADL-TTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAA 621 A ET T +PV NPA TVG V A + TA + ATPWNA A RAEVLN+AA Sbjct: 545 AGDAETGAT--DPVINPARPGDTVGSVTWATSGTVATACTVATPWNADAAERAEVLNKAA 602 Query: 622 DLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAEPPVGVFTCISPWNF 681 DLYEA+YGELFALL REAGK+L D VAELREAVDFLRYYAAR P GVF CISPWNF Sbjct: 603 DLYEAHYGELFALLAREAGKSLLDAVAELREAVDFLRYYAARAEGPDPQGVFACISPWNF 662 Query: 682 PLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAGAVGGA 741 PLAIF+GQIAAAL GNAVLAKPAEQTPLIA+RA+ LLHEAGVP +ALQLLPGAG VG A Sbjct: 663 PLAIFTGQIAAALTTGNAVLAKPAEQTPLIAYRAVQLLHEAGVPTTALQLLPGAGDVGAA 722 Query: 742 LTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQS 801 LTS+ V GVAFTGST TA I +MA+HL PGAPLIAETGGLNAMIVDSTALPEQAVQ+ Sbjct: 723 LTSNPAVKGVAFTGSTETAQIIHRSMAKHLAPGAPLIAETGGLNAMIVDSTALPEQAVQA 782 Query: 802 IIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETA 861 I+ESAFQSAGQRCSALRCLY+QEDIA++ ++ML GAMDAL +GDPW TD GP ID A Sbjct: 783 IVESAFQSAGQRCSALRCLYVQEDIAESFVEMLTGAMDALVIGDPWIYGTDVGPAIDAEA 842 Query: 862 RAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQ 921 R GI++++DAA EGRVL + P GGTFV PTLI ++GI LE+EIFGPVLH+ FKS+ Sbjct: 843 RDGIISYVDAAEVEGRVLHRLPLPGGGTFVPPTLIRVSGIADLEREIFGPVLHIATFKSK 902 Query: 922 DLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEG 981 D+D +I IN T YGLTFGL TRIDDRVQ++ ++I AGN+YVNRNQIGAIVGSQPFGGEG Sbjct: 903 DIDTVIDAINGTDYGLTFGLQTRIDDRVQHVSEQIKAGNIYVNRNQIGAIVGSQPFGGEG 962 Query: 982 LSGTGPKAGGPFYMMRFCAPDRQKSVDSWPS--DAPAMTMLPAPTGQPMQEITTSLPGPT 1039 LSGTGPKAGGP Y+ RF + D WPS +T G T+LPGPT Sbjct: 963 LSGTGPKAGGPNYLARFRRHPADTAGDVWPSQDSKDRLTKALTSAGGKASATKTTLPGPT 1022 Query: 1040 GESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVI 1099 GESN L+ +AR P+LCLGPGP+A AQARAV ALGG A++A G + L +E + G I Sbjct: 1023 GESNVLTAMARGPILCLGPGPEAAKAQARAVEALGGIAVKAEGGIAPDWLADLE-SEGAI 1081 Query: 1100 WWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGG 1156 WWGD+ TAR + + LA R GPILPLI G+PDK ERHVCVDTTA+GGNA LL G Sbjct: 1082 WWGDDETARALRTELASRKGPILPLITGMPDKGHACHERHVCVDTTASGGNAQLLSG 1138 Lambda K H 0.317 0.132 0.387 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: 3260 Number of extensions: 147 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: 1158 Length of database: 1140 Length adjustment: 46 Effective length of query: 1112 Effective length of database: 1094 Effective search space: 1216528 Effective search space used: 1216528 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 (21.7 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