Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_084271505.1 AYX06_RS07690 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::azobra:AZOBR_RS23695 (1235 letters) >NCBI__GCF_001580365.1:WP_084271505.1 Length = 1168 Score = 253 bits (647), Expect = 5e-71 Identities = 299/971 (30%), Positives = 418/971 (43%), Gaps = 114/971 (11%) Query: 262 ISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIG--LNIDAEEADRLELSLDL 319 +SIK+S+ +S D + E++ ++ L A + +N+D EE L+++L + Sbjct: 196 VSIKVSSTVAPHSAWAFDEAVAEVVEKLTPLYARAVSFSTPKFINLDMEEYKDLDMTLAV 255 Query: 320 MESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDL-----ARRS--GHRLMIRLVKGA 372 + P G V+Q Y P + +I L ARR+ G R+ +R+VKGA Sbjct: 256 FTRILDQPQFQDLEA-GIVLQTY---LPDALQAMIRLQEWAQARRAAGGARVKVRVVKGA 311 Query: 373 YWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAP--EAVFPQFATHNAQTLAT 430 E A L P + K +D Y L +AV A HN +A Sbjct: 312 NLPMEQVEASLHDWP-LATWGTKQDSDTHYKRVLNYALQPEHADAVRIGVAGHNLFDIAF 370 Query: 431 IYEMAGSDFQVGKYEFQCLHGMGE---PLYKEVVGPLKRPCRIYAPV---GTHETLLAYL 484 + +A +F+ L GM K VG L +Y PV + +AYL Sbjct: 371 AWLLASERGVTEAIDFEMLLGMATGQAQAVKRDVGSLL----LYTPVVHPAEFDVAIAYL 426 Query: 485 VRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERA 544 +RRL E + +F++ + + + + + R +A A + LP Sbjct: 427 IRRLEEGASQENFMSAVFELSANEELFEREK---NRFLASLAALDDTVPLPHR------- 476 Query: 545 NSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVT 604 + + L L A A T P +A G+A R P G+ T Sbjct: 477 -------TQDRRLPELPAPTDGFAN-TPDTDPAVAANRDWGRAILDRVPGS---TAGTAT 525 Query: 605 EASEALVAE-----AFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREA 659 A+ AL E A+AA WAA +RA L RA + + R LL + EA Sbjct: 526 VAAAALQTEEQLDRVIDAALAAGRGWAALTGAQRAEVLHRAGEALAARRAELLEVAAAEA 585 Query: 660 GKSLPNAIAEVREAIDFLRYYGAQVR--DRFDNATHRPLGPVVCISPWNFPLAIFSGQIA 717 GK+L A E+ EAIDF YY + R D D AT P V PWNFP+AI +G Sbjct: 586 GKTLDQADPEISEAIDFAHYYAERARELDEVDGATFLPSRLTVVTPPWNFPVAIPAGSAL 645 Query: 718 AALAAGNPVLAKPAEETP---LIAAEAV-RILHAAGIPAGALQLLP-GAGEVGAALVGHE 772 AALAAG+PV+ KPA T + AEA+ L A+GIP L L+ +G L+ H Sbjct: 646 AALAAGSPVVFKPAGPTKRCGAVVAEAIWEALDASGIPRDVLALVDLEERALGRQLISHP 705 Query: 773 AVRGVMFTGSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVI 832 +V ++ TG+ E A L + + +PL+AET G+NA++V SA + DV Sbjct: 706 SVDRLILTGAYETAELFR--------SFRSDLPLLAETSGKNALVVTPSADFDLAAKDVA 757 Query: 833 ASAFDSAGQRCSALRILCLQEDVA--DRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEA 890 SAF AGQ+CSA ++ L VA R L A+ L + P A +GP ++E A Sbjct: 758 YSAFGHAGQKCSAASLVILVGSVAKSKRFRNQLVDAVSSLTVDYPTNPAAQMGP-LTEPA 816 Query: 891 RATIAAHIEAMRAKGRNVEFLPLPAETAD-GTFIAP---TVIEIGGIHELEREVFGPVLH 946 + ++A+ +L P + D G +P T ++ G L E FGPVL Sbjct: 817 EGKL---LQALTTLEDGQSWLIEPQQLDDTGKLWSPGVRTGVQRGSEFHLV-EYFGPVLG 872 Query: 947 VVRFHRDDLDALVDSINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGV 1006 V+ + L+ V N YGLT GLH+ I + AGNVYVNR GA+V Sbjct: 873 VMT--AETLEEAVAIQNEVDYGLTGGLHSLDPEEIGYWLEHVQAGNVYVNRGITGAIVQR 930 Query: 1007 QPFGGHGLSGTGP--KAGGPLYLSRLLSRRPKGWLEFRG-----PDAARAAGLAYGEWLR 1059 QPFGG S GP KAGGP YL L P RG DAA A LA R Sbjct: 931 QPFGGWKKSAVGPGTKAGGPSYLMGLGEWEP---APLRGDGRPVTDAAVADLLAAARAGR 987 Query: 1060 AKGFTAEASRCAGYVARSAIGGGAELNGPVGE-RNLYELHGRGRVLLLPQT--------R 1110 A G T + + RS AE G + LY R L LP T Sbjct: 988 A-GVTEQEAGTLEQALRSDEAAWAEEFGVARDVSQLYAERNVFRYLPLPVTVRLSEGEPL 1046 Query: 1111 TGLLLQLGAVLATGN----SAAVDAPPDLAELL--RGLPPALAARVRTTADW----RDVG 1160 LL +GA L G S+A++ P + +L RG+P RV A W ++G Sbjct: 1047 ADLLRVVGAGLRAGAELSVSSALELPAAVRSVLTGRGVP----VRVEDDAAWLARAAELG 1102 Query: 1161 PLAAVLVEGDR 1171 L+ GDR Sbjct: 1103 GGRVRLIGGDR 1113 Lambda K H 0.319 0.136 0.396 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: 3182 Number of extensions: 167 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: 1235 Length of database: 1168 Length adjustment: 47 Effective length of query: 1188 Effective length of database: 1121 Effective search space: 1331748 Effective search space used: 1331748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (27.3 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