Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate WP_012169494.1 AZC_RS04935 GMC family oxidoreductase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >NCBI__GCF_000010525.1:WP_012169494.1 Length = 522 Score = 207 bits (526), Expect = 1e-57 Identities = 165/572 (28%), Positives = 257/572 (44%), Gaps = 83/572 (14%) Query: 17 IVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNPWDFKHAGKLTEEQKR 76 +++GSG GG EL +KG++V++LE G E + + + W+ T+ + Sbjct: 13 VIVGSGAGGGTLGNELAQKGIKVVILEAGARNE----IQDFVNDEWESFAQLAWTDMRVA 68 Query: 77 THPVQ-KRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQSYRLSDHN 135 + + RD+P A W V VGG ++ W S R H Sbjct: 69 SGSWRVARDFPNLPA---WIVKS------------------VGGSTVHWAGASLRFEQHE 107 Query: 136 FEDNARDGHGS-------DWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMD 188 F+ A +G DWP+ AEL P+Y AE G++ + +P + Sbjct: 108 FK--AASAYGGIKGANLLDWPITKAELDPYYAKAEDKMGVTRTNN----------IPGLP 155 Query: 189 LNIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFGAYFSTQS 248 N EK ++A + ++ GR+A + P GRG+CQ C +GC GA +ST Sbjct: 156 GNNNEKVLEAGARKIGYKD--FSTGRMAINSQPRDGRGSCQQIGFCFQGCKSGAKWSTLY 213 Query: 249 STLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFVNGSTL 308 + +P AT L +RP V I +D + K V+ D ET T A++V V G+++ Sbjct: 214 TEIPKGEATGNLEVRPNCHVAKIEHDANGK-VTAVVYFD-ETGATQRQKARVVAVAGNSI 271 Query: 309 GSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRANGIYI 368 S +LLNS S PNGL N SGQ+G N M H +G +K + R + Sbjct: 272 ESPRLLLNSASSLFPNGLANSSGQVGRNYMRH-----VTGSVYAAFEKPVHMYRGTTM-- 324 Query: 369 PRYQNIGNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKWSM------- 421 I D+ + G G+ GG ++ LS G PG W Sbjct: 325 ---AGIIRDEARHDPGRGFAGGY-------EMETLSLGLPFMAAFLNPGAWGRSFTSAME 374 Query: 422 ------GLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAE 475 G+ GE +P +N + +DK KDK+G PV + + N+ MR A Sbjct: 375 NYPRMAGMWLVGEDMPQEKNAITLDKEAKDKFGLPVANVHYDDHSNDVAMRNHGYQQGAA 434 Query: 476 MLEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCM 535 + E G ++T+ YP + H +GT RM P+ V+NK+ Q H++ N+FV+DGS Sbjct: 435 LYEAVGA--VQTYPTTPYP--STHNLGTNRMSEKPRDGVVNKFGQSHDIKNLFVSDGSQF 490 Query: 536 PSIACQNPSLTFMALTARACDYAVKELKKKNI 567 + A NP+LT +AL R D+ + +++++I Sbjct: 491 TTSAACNPTLTIVALAIRQADHMAELMRRRDI 522 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: 771 Number of extensions: 46 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 567 Length of database: 522 Length adjustment: 35 Effective length of query: 532 Effective length of database: 487 Effective search space: 259084 Effective search space used: 259084 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