Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_068010021.1 PsAD2_RS20095 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::Marino:GFF2744 (1209 letters) >NCBI__GCF_001623255.1:WP_068010021.1 Length = 1212 Score = 1353 bits (3503), Expect = 0.0 Identities = 695/1210 (57%), Positives = 871/1210 (71%), Gaps = 12/1210 (0%) Query: 8 TPELVDSRQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIM 67 TPE++ R IRD YL DE +V+ E+I+ Q+ +A R+ S AA+L++ +R N TIM Sbjct: 6 TPEII--RDKIRDNYLPDEKQVVQELISSLQMDEAARERASRGAADLIQDLRANTSPTIM 63 Query: 68 EKFLAEYGLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINT 127 E FL EYGL+T+EG+ALMCLAEALLRVPD TI LI DKIT AWG H+G++SS LIN Sbjct: 64 ESFLGEYGLSTQEGIALMCLAEALLRVPDAQTIDALIADKITPSAWGEHLGRSSSTLINA 123 Query: 128 ATVALLMTSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEA 187 +T ALL+T +L ++ VG T+R ++KR GEPV+RT QAMKE+GRQFVLGR I EA Sbjct: 124 STWALLLTGKVLAPDDQGLVG-TIRGVVKRMGEPVVRTAVAQAMKELGRQFVLGRTIREA 182 Query: 188 QDEAKEYMAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKG-DVRKNPGISV 246 A+ G+TYSYDMLGEAA TD DAKRY+ SYS AI +++ K +R+NPGISV Sbjct: 183 MRNARVEEGNGFTYSYDMLGEAACTDADAKRYHLSYSKAITALSSNCKHHSIRENPGISV 242 Query: 247 KLSALLARYEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELV 306 KLSAL RYE+ +ERVM EL+PR L+ A ++NMGFNIDAEE DRLD+SLDVIE L+ Sbjct: 243 KLSALHPRYEFAKRERVMKELVPRTLSLIMLAKSSNMGFNIDAEEADRLDISLDVIEALL 302 Query: 307 ADPELAGWDGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVM 366 ADP GWDGFGVVVQA+G R++ V+DWLY +A+KYDRK MVRLVKGAYWD EIKRAQ + Sbjct: 303 ADPATEGWDGFGVVVQAFGPRATHVIDWLYAVAQKYDRKIMVRLVKGAYWDTEIKRAQTL 362 Query: 367 GLNGFPVFTRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYE 426 G+ G+PVFTRK +D+SF CA KLL MT+RIYPQFATHNAHSV+ ILE+AK +++YE Sbjct: 363 GIEGYPVFTRKVSTDLSFTVCAEKLLAMTDRIYPQFATHNAHSVATILELAKNLPLNSYE 422 Query: 427 FQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKR 486 FQRLHGMGE+LH +K G CRIYAPVG HKDLLAYLVRRLLENGANSSFV+QI D+ Sbjct: 423 FQRLHGMGEALHERTMKKHGSNCRIYAPVGAHKDLLAYLVRRLLENGANSSFVHQIRDES 482 Query: 487 ITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGA 546 ++P+ IA+DP++ +E G IS+ I P L+G R+N+KGWD+TDP + + + Sbjct: 483 VSPKAIAQDPLMHIEAYGEQISNAKIALPPALYGSGRKNAKGWDLTDPKQETQYVESMKS 542 Query: 547 YKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWS 606 + +W+G P+IA V V+NPAD D VGHV A+ ++ A+T+A A + W+ Sbjct: 543 FLTTKWEGHPVIAASVKNATAIAVKNPADLRDTVGHVATATPEQIEAALTAAHAGCKEWT 602 Query: 607 AKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIR 666 K+A++RA +RK DL EEN +E+FAL TREAGK+ +DA+ E+REAVDF +YYANEAIR Sbjct: 603 EKNAQDRAVVLRKAADLLEENASEIFALLTREAGKTYMDAINELREAVDFGRYYANEAIR 662 Query: 667 YKD---SGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELM 723 ++ DARG + CISPWNFPLAIF+GQI A LAAGN V+AKPA QT L+A AV LM Sbjct: 663 LEERDGKSDARGPVTCISPWNFPLAIFSGQIFAALAAGNPVLAKPAPQTPLIATYAVGLM 722 Query: 724 HQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLV 783 HQAGIP A+QL+PG G VGAALTSD RV+GVCFTGSTATAQ IN+ M + P APL+ Sbjct: 723 HQAGIPVQALQLLPGAG-EVGAALTSDKRVAGVCFTGSTATAQHINRAMANALCPTAPLI 781 Query: 784 AETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAM 843 AETGGLNAMIVDSTALPEQ VRDV+ASSFQSAGQRCSALRMLYVQ DI + EML GAM Sbjct: 782 AETGGLNAMIVDSTALPEQAVRDVIASSFQSAGQRCSALRMLYVQEDIFEDFKEMLLGAM 841 Query: 844 EELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSV 903 EL +GDP LSTDVGPVID A+ KI HC+K+ G++LK++K P KG FV+P ++ + Sbjct: 842 AELELGDPSALSTDVGPVIDAAAQSKIDAHCKKWAEKGRVLKQLKAPNKGHFVAPTLIHL 901 Query: 904 SGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKV 963 GIEEL EEIFGPVLH+ATF+A+ ID+ +D IN +GYGLTFG+H+RVD RV+ + R+KV Sbjct: 902 DGIEELGEEIFGPVLHIATFKAEEIDQTIDAINGQGYGLTFGLHTRVDSRVQHVVERVKV 961 Query: 964 GNTYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLKGETVEREADSNARKVDAK 1023 GN YVNRNQIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF + +T E+ + + A+ Sbjct: 962 GNLYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPHYLSRFARADTKSAESVTLHKSFTAE 1021 Query: 1024 QLQKLIGQLDKLKASRPEARMDAIRPIFGNVPEPLDAHVEA----LPGPTGETNRLSNHA 1079 + K G + AR + +F L + +PGPTGE+NRL + Sbjct: 1022 DIFKAHGAVRTNNWESNSARFTELATLFKQEAHLLHRAAQEQAYDMPGPTGESNRLYSAP 1081 Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139 RG VLCLGPD E+ Q AL+ GN V+ + G + + PIV +G L Sbjct: 1082 RGTVLCLGPDTESLKHQVVLALAAGNSVIAVGQGAEKLAASLRSFSAPIVALEGQLAEGT 1141 Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199 L + G +A+ + + LK + LA RDGAL+ LI E +R+ +ERHLC+DTTA+G Sbjct: 1142 LTKLQGIDAIAANHSEEDLKVMKGELADRDGALMQLIMERNQIERYQLERHLCIDTTASG 1201 Query: 1200 GNASLIAASE 1209 GN SL+AASE Sbjct: 1202 GNTSLLAASE 1211 Lambda K H 0.316 0.133 0.378 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: 3313 Number of extensions: 142 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: 1209 Length of database: 1212 Length adjustment: 47 Effective length of query: 1162 Effective length of database: 1165 Effective search space: 1353730 Effective search space used: 1353730 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: 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