Align L-arabinose 1-dehydrogenase (NAD(P)(+)); D-galactose 1-dehydrogenase; EC 1.1.1.376; EC 1.1.1.120; EC 1.1.1.48 (characterized)
to candidate WP_012334361.1 M446_RS22210 gfo/Idh/MocA family oxidoreductase
Query= SwissProt::Q53TZ2 (309 letters) >NCBI__GCF_000019365.1:WP_012334361.1 Length = 313 Score = 326 bits (835), Expect = 5e-94 Identities = 170/302 (56%), Positives = 205/302 (67%) Query: 7 LGVVGIGKIARDQHLPAIDAEPGFKLTACASRHAEVTGVRNYRDLRALLAAERELDAVSL 66 + +VG+GKIARDQHLPAI A PG L A A A + + + L ALL + DAV+L Sbjct: 10 IALVGLGKIARDQHLPAIAATPGLDLAATAGPGAGLENLPHAPTLAALLESGPPFDAVAL 69 Query: 67 CAPPQVRYAQARAALEAGKHVMLEKPPGATLGEVAVLEALARERGLTLFATWHSRCASAV 126 C PP+ R A A AAL AGKHV+LEKPP ATLGE+ L A AR GL+LF WHSR A AV Sbjct: 70 CTPPRGRGALAAAALAAGKHVLLEKPPAATLGEILPLAAQARAAGLSLFCAWHSRFAPAV 129 Query: 127 EPAREWLATRAIRAVQVRWKEDVRRWHPGQQWIWEPGGLGVFDPGINALSIVTRILPREL 186 EPAR L R IRAV+V W+ED+R WHPGQ WI EPGGLGVFDPGINALS+VT +LPR + Sbjct: 130 EPARAALRDRPIRAVRVDWREDIRVWHPGQDWILEPGGLGVFDPGINALSLVTHLLPRPV 189 Query: 187 VLREATLIVPSDVQTPIAAELDCADTDGVPVRAEFDWRHGPVEQWEIAVDTADGVLAISR 246 + A L P+D Q PIAA LD AD G+P+RAEFD+ + W+I T G+L +S Sbjct: 190 QVTGADLAFPADRQAPIAAALDLADAAGLPIRAEFDFLQAGPQTWDIRFATERGLLLVSG 249 Query: 247 GGAQLSIAGEPVELGPEREYPALYAHFHALIARGESDVDVRPLRLVADAFLFGRRVQTDA 306 GGA+LS+ G P+ PE EY LY F L++R ES+ D+ PL LVADAF+ GRR A Sbjct: 250 GGARLSLDGVPIPTAPEAEYRGLYRRFRDLVSRRESEADLAPLGLVADAFMIGRRRTVAA 309 Query: 307 FG 308 FG Sbjct: 310 FG 311 Lambda K H 0.321 0.136 0.421 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: 352 Number of extensions: 12 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: 309 Length of database: 313 Length adjustment: 27 Effective length of query: 282 Effective length of database: 286 Effective search space: 80652 Effective search space used: 80652 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 (21.9 bits) S2: 48 (23.1 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