Align Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized)
to candidate WP_011777563.1 MVAN_RS01230 aldehyde dehydrogenase
Query= SwissProt::H1ZV37 (478 letters) >NCBI__GCF_000015305.1:WP_011777563.1 Length = 491 Score = 414 bits (1065), Expect = e-120 Identities = 224/471 (47%), Positives = 302/471 (64%), Gaps = 3/471 (0%) Query: 8 IFVGGQWIAPKSTQRSNILNASTEELVGSVPKCNNEDMDRAVAAAREAMRSLAWAGLDGK 67 +F+GG+W+ P ++ + + +T ELVG VP + D+D A AAAREA + W + Sbjct: 14 LFIGGKWVEPATSDVIEVHSPATGELVGKVPLASAADVDAACAAAREAFDNGPWPHMSPA 73 Query: 68 GRAQHLRRFADAVERRGQQLARSVSLQNGMPINVADQLESAFVVSLLRYYASLAENLVEE 127 R + L R +E R +L ++ + G P + D ++ +S ++YA A+ + Sbjct: 74 ERGEILGRAVKIMEERADELKFLLAAETGQPPTIVDMMQYGAAMSSFQFYAGAADKFTWQ 133 Query: 128 EARPSPTGSTTLVRRDPVGVVGAIIPWNFPVALSIFKIAPALAAGCAVVVKPSSGTVLDS 187 + R G T LV R+PVGVVGA+ WN P L+ K+ PAL AGC VV+KP++ T L Sbjct: 134 DIRDGVYGQT-LVVREPVGVVGAVTAWNVPFFLAANKLGPALLAGCTVVLKPAAETPLSV 192 Query: 188 YVLAEAAAEAGLPPGVINWVPGDRGIGSHLVSHPGVDKVAFTGSTSAGRIIAEACARLLR 247 + +AE EAGLP GV++ VPG G L ++P +DK FTGS+ G+ IA+ A L+ Sbjct: 193 FAMAEMFVEAGLPEGVLSIVPGGPETGQALTANPNLDKYTFTGSSGVGKEIAKIAADKLK 252 Query: 248 PVTLELGGKSAAIVLEDADLDALIRSLPMSSVLNNGQACFSCTRILAPAGRYDEVVDAIA 307 P TLELGGKSAAI+LEDADLD+ + L S ++N+GQAC TRILAP RYDEVV+ +A Sbjct: 253 PCTLELGGKSAAIILEDADLDSTLPMLVFSGLMNSGQACVGQTRILAPRSRYDEVVEKLA 312 Query: 308 GAVSAYSVGDALDRATVVGPMASAAHRDSVQRYIELGTGE-ARLVVGGGR-TSQDRGWFV 365 A + + G + A ++GP+ S RD V+ YI+ G E AR+V GGGR D GW+V Sbjct: 313 AAAAGMAPGLPDNPAAMIGPLISEKQRDRVEGYIKKGIEEGARVVTGGGRPEGLDSGWYV 372 Query: 366 QPTVFADVDNRSRIAREEIFGPVLSIIRYEGEDEAVEIANDSEYGLGGTVWSTDHDHAVT 425 QPTVFADVDN IA+EEIFGPVL++I YE ED+AV IANDS YGL G+V++TD+D A+ Sbjct: 373 QPTVFADVDNSMTIAQEEIFGPVLAVIPYEDEDDAVRIANDSVYGLAGSVYTTDNDRALK 432 Query: 426 IARRMETGTVGINGYMPDLNAPFGGVKSSGMGRELGPESIGAYQRYKSVYL 476 IARR+ TGT +N Y D APFGG K+SG+GRE G E I AY KS+ L Sbjct: 433 IARRIRTGTYAVNMYAFDPCAPFGGFKNSGIGRENGWEGIEAYCEPKSILL 483 Lambda K H 0.317 0.134 0.391 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: 629 Number of extensions: 29 Number of successful extensions: 3 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: 478 Length of database: 491 Length adjustment: 34 Effective length of query: 444 Effective length of database: 457 Effective search space: 202908 Effective search space used: 202908 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: 52 (24.6 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