Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate WP_057509068.1 ABB28_RS13240 GMC family oxidoreductase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >NCBI__GCF_001431535.1:WP_057509068.1 Length = 562 Score = 712 bits (1837), Expect = 0.0 Identities = 334/561 (59%), Positives = 424/561 (75%), Gaps = 3/561 (0%) Query: 10 AENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNPWDFKHAGK 69 A+N YDAIV+GSGISGGWAAKELTEKGL+VLMLERG NIEH+ GY AMK WDF H + Sbjct: 2 ADNHYDAIVVGSGISGGWAAKELTEKGLKVLMLERGRNIEHVKGYVNAMKEAWDFPHRNR 61 Query: 70 LTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQSY 129 T+ K PV RDY E E W ++ + PY E KRFDW+RG+HVGG+SLMWGRQSY Sbjct: 62 PTQAMKADFPVLMRDYGLAENLEGMWADEKDSPYIETKRFDWFRGYHVGGRSLMWGRQSY 121 Query: 130 RLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMDL 189 RLSD +FE N +DG +DWP+RYA+++PWYD+ E+FAGI+G++E PDG+FLPP+ L Sbjct: 122 RLSDLDFEANLKDGIATDWPIRYADIAPWYDHVEKFAGIAGTREGLDVLPDGEFLPPIPL 181 Query: 190 NIVEKSVKARIEEHYKRERIMMIGRVANLTVP--HKGRGNCQYRNLCSRGCPFGAYFSTQ 247 NIVEK V ARI++ + R M+ R AN+T P +GR NCQYRN C GCPFGAYFSTQ Sbjct: 182 NIVEKDVAARIKKAFGGTRHMIHSRTANITQPKVEQGRVNCQYRNKCILGCPFGAYFSTQ 241 Query: 248 SSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFVNGST 307 S+TLPAAM T LTLRP+SIV ++YDKD K+A+GV +IDAE +T ++ A ++F+N S+ Sbjct: 242 SATLPAAMKTGNLTLRPFSIVKEVLYDKDHKRARGVEIIDAENGQTYQYTANVIFLNASS 301 Query: 308 LGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRANGIY 367 S+++L+NS ++ GLG+ SG+LGHN+MDHHF GASG EG+DDKY +GRR G Y Sbjct: 302 FNSSWLLMNSATDVWDGGLGSSSGELGHNVMDHHFGAGASGRVEGYDDKYYFGRRPCGFY 361 Query: 368 IPRYQNIG-NDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKWSMGLGGF 426 +PR++N+G NDKR Y RGFGYQGGASR W ++AEL+ GA+LK +T PG W +G+ GF Sbjct: 362 VPRFRNVGTNDKRGYSRGFGYQGGASRNGWSREIAELNIGAELKDALTLPGDWRIGMTGF 421 Query: 427 GEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEMLEKAGMKNIK 486 GEMLP+++N + +D KKDKWG PVLA+D + NE MR DM DAAEMLE AG+K+++ Sbjct: 422 GEMLPHHDNTIRLDSEKKDKWGLPVLAMDVSLRANETAMRKDMAADAAEMLEAAGVKDVE 481 Query: 487 TFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMPSIACQNPSLT 546 DN PG IHEMGTARMG D ++SVLN+ NQ+ + NV+VTDG+CM S AC NPSLT Sbjct: 482 MHDNDYAPGKGIHEMGTARMGRDRRSSVLNQHNQVWDAPNVYVTDGACMTSSACVNPSLT 541 Query: 547 FMALTARACDYAVKELKKKNI 567 +MALTARA D+AV+ELK N+ Sbjct: 542 YMALTARAADHAVRELKAGNL 562 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: 1057 Number of extensions: 47 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: 567 Length of database: 562 Length adjustment: 36 Effective length of query: 531 Effective length of database: 526 Effective search space: 279306 Effective search space used: 279306 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 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