Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate CA265_RS16770 CA265_RS16770 GMC family oxidoreductase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Pedo557:CA265_RS16770 Length = 578 Score = 239 bits (611), Expect = 2e-67 Identities = 185/593 (31%), Positives = 280/593 (47%), Gaps = 56/593 (9%) Query: 9 KAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIE-HITGYETAMKNPWDFKHA 67 K+ YDAI++GSG GG AA L G +VL+LE G N + + ++ +K PW+ Sbjct: 8 KSPTVYDAIIVGSGAGGGMAAYVLAHAGQKVLLLEAGQNFDPRLDSHQ--LKWPWESPRR 65 Query: 68 GKLTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKR--FDWYRGFHVGGKSLMWG 125 G T T P D Y W + E PYT+ + F+W+R +GG++ WG Sbjct: 66 GAST-----TRPFGDFDASYGG-----WELEGE-PYTQKNKSEFEWFRSRMLGGRTNHWG 114 Query: 126 RQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLP 185 R S R+ +F+ +DG WP+ YA++ P+YD +R GI G+ E PDG F+ Sbjct: 115 RISLRMGPEDFKP--KDGLTDAWPITYADVKPFYDKVDRMIGIYGTAEGLENEPDGIFMK 172 Query: 186 PMDLNIVEKSVKARIEEHYKRERIMMIGRVANLT--VPHKG-RGNCQYRNLCSRGCPFGA 242 P + E +K E+ + ++ GR + LT +P+ R C Y C R C Sbjct: 173 PPKPRLNELFIKKGAEKAGVK---VITGRGSVLTEALPNNNDRAPCFYCGQCGRSCKVYG 229 Query: 243 YFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVF 302 FS+ S + A+ T LT+ ++V +I DKD AKGV ++ + + + K+V Sbjct: 230 DFSSSSCLVNPAVKTGNLTVITDAMVREVITDKDGS-AKGVSYVNRKDLQEYQVNGKLVI 288 Query: 303 VNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRR 362 + S S +LLNS S +HPNGL N SG +G L D SG D+ Y Sbjct: 289 LGASACESARILLNSKSTSHPNGLANSSGVVGKYLHDST-GASVSGFLPQLMDRKRYNED 347 Query: 363 ANG---IYIPRYQNIGNDKRDYLRGF-------------GYQGGASRANWQ-----GDVA 401 G IY P + + N K ++ RG+ G+ GG ++ N G + Sbjct: 348 GLGSVHIYSPWW--LDNRKLNFPRGYHIEYWGGMGMPAYGFGGGVAQMNGMVPGRDGKMK 405 Query: 402 ELS-FGADLKQKMTTPGKWSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKE 460 E +G LK +G+ G G + +N ID DK+G PVL + ++ + Sbjct: 406 EAGGYGKSLKDDYRRFYGTGVGMAGRGTAIAREDNYCEIDPNTVDKYGIPVLRFNYKWAK 465 Query: 461 NEKKMRVDMMNDAAEMLEKAGM---KNIKTFDNG---CYPGMAIHEMGTARMGNDPKTSV 514 +E M ++++ G I+ D PG IHE+GT RMG+DPK S Sbjct: 466 DEILQAKHMQETFLSIMKEMGAVVTSEIQGADTNYGLLNPGKIIHEVGTIRMGDDPKKSA 525 Query: 515 LNKWNQMHEVNNVFVTDGSCMPSIACQNPSLTFMALTARACDYAVKELKKKNI 567 LNK+ Q H+ N+FV D +N + T +AL+ R +Y + + KK+NI Sbjct: 526 LNKYCQAHDCKNLFVVDAGPFVQQGDKNATWTILALSMRTAEYILAQKKKQNI 578 Lambda K H 0.317 0.134 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: 895 Number of extensions: 65 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: 567 Length of database: 578 Length adjustment: 36 Effective length of query: 531 Effective length of database: 542 Effective search space: 287802 Effective search space used: 287802 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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