Align β-galactosidase (BgalH) (EC 3.2.1.23) (characterized)
to candidate WP_057507603.1 ABB28_RS05105 amine oxidase
Query= CAZy::AFA35120.1 (389 letters) >NCBI__GCF_001431535.1:WP_057507603.1 Length = 1270 Score = 216 bits (551), Expect = 2e-60 Identities = 129/338 (38%), Positives = 176/338 (52%), Gaps = 13/338 (3%) Query: 11 FLGGFECSTHRRRDGRRLDLIAGTRHDQYASNDYAALAHHAIHSVRDGMRWHLIETAKGR 70 ++GGFE + H GR L + + H DY L +VR+ + W E G Sbjct: 3 WIGGFEGADHVNGSGRALSMAVDSGHLARLDTDYRRLRRMGFSAVRESLGWRTCEQGDG- 61 Query: 71 YDWSSVLPMIRAAKAQRTEVIWDLCHYGWPDDIDIF---KAEFVERFAAYAAAATRLLRN 127 +++ S+ ++AA+ E+ W L HYG P D+D+ K FVERFAA+ A L + Sbjct: 62 FNFQSLHARMQAAERAGLEIRWTLMHYGVPADLDLLDGNKTAFVERFAAFCQATATALAD 121 Query: 128 EGIEAP-LITPLNEISFWAWAGGSVAHFNPTVRRRGDE---LKRQLVRAAIAAMEAIREI 183 +P LI P+NEISF +WA +P R E LK L+RAA+A A R + Sbjct: 122 YASPSPRLINPINEISFLSWAATHTGLIHPHAGDRPAEAGRLKSLLIRAALAGCSAFRRV 181 Query: 184 LPKARFIQVDPIIHVVSRSTRRRDRERAERLKFEQYTAWDMLCGAQHPELGGKPAYLDIM 243 P AR + V+P+IHVV+ R++AERL Q+ D L G P LGG P Y+D++ Sbjct: 182 DPTARMLWVEPLIHVVAPLASPALRQQAERLHAGQFEVLDALMGRVQPSLGGAPGYVDLI 241 Query: 244 GVNYYPHNQWYANRQDIPMD----SPDYRPFHKLLADAFQRYGKPLLIAETGAESERRVP 299 GVNYY NQW A Q P+D P PF +LL QRYG PL ++ET R Sbjct: 242 GVNYYHGNQWEAGSQR-PLDWHRADPQRVPFSRLLVKLQQRYGVPLTLSETSHVGCGRGA 300 Query: 300 WVRYVCEQVDIALRQNIPVEGICLYPITDYPGWENNRH 337 W+ + +QV A +EGICLYP+ D P WE+ H Sbjct: 301 WLSDIAQQVRYAADAGARLEGICLYPVVDRPDWESPLH 338 Lambda K H 0.324 0.138 0.442 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: 1335 Number of extensions: 65 Number of successful extensions: 5 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: 389 Length of database: 1270 Length adjustment: 39 Effective length of query: 350 Effective length of database: 1231 Effective search space: 430850 Effective search space used: 430850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 54 (25.4 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