Align β-galactosidase (BgalH) (EC 3.2.1.23) (characterized)
to candidate AZOBR_RS31660 AZOBR_RS31660 beta-glucosidase
Query= CAZy::AFA35120.1 (389 letters) >FitnessBrowser__azobra:AZOBR_RS31660 Length = 387 Score = 473 bits (1217), Expect = e-138 Identities = 220/368 (59%), Positives = 266/368 (72%) Query: 1 MHQPSLFKSFFLGGFECSTHRRRDGRRLDLIAGTRHDQYASNDYAALAHHAIHSVRDGMR 60 MH P+LF S FLGGFECSTHRR DGRRLDLIA T HD+ A+ DY +A H + SVRDG R Sbjct: 1 MHIPTLFDSAFLGGFECSTHRRHDGRRLDLIAATGHDRLAAEDYRRMAAHGLRSVRDGAR 60 Query: 61 WHLIETAKGRYDWSSVLPMIRAAKAQRTEVIWDLCHYGWPDDIDIFKAEFVERFAAYAAA 120 WHLIET G YDWSS+LPM+RAA+ +VIWDLCHYGWPDDIDI++ FVERFA +A A Sbjct: 61 WHLIETTPGHYDWSSLLPMVRAAREAGVQVIWDLCHYGWPDDIDIWRPAFVERFARFAGA 120 Query: 121 ATRLLRNEGIEAPLITPLNEISFWAWAGGSVAHFNPTVRRRGDELKRQLVRAAIAAMEAI 180 A LLR+EG+E P P+NEIS+WAWAGG + FNP RRG ELK QLVRA+IAA++AI Sbjct: 121 AAALLRDEGVETPAYCPVNEISYWAWAGGDMKRFNPMAERRGAELKHQLVRASIAAIDAI 180 Query: 181 REILPKARFIQVDPIIHVVSRSTRRRDRERAERLKFEQYTAWDMLCGAQHPELGGKPAYL 240 R P+AR +QVDP+I+V+ R RR D AE + QY AWDM+ G P LGGKP YL Sbjct: 181 RAADPRARIVQVDPVINVLPRPDRRGDAGAAEEARLAQYEAWDMIGGYAWPGLGGKPEYL 240 Query: 241 DIMGVNYYPHNQWYANRQDIPMDSPDYRPFHKLLADAFQRYGKPLLIAETGAESERRVPW 300 D++GVNYY NQW+ I D P YRPF +LA+ QRYG+P+L+AETGAE + R PW Sbjct: 241 DVIGVNYYSDNQWFLKGGTIGRDDPRYRPFADILAEVHQRYGRPVLVAETGAEGDARAPW 300 Query: 301 VRYVCEQVDIALRQNIPVEGICLYPITDYPGWENNRHCRTGLLGYADAQGQRPVFSPLAD 360 + YV +V AL+ ++PVEG+CLYPI DYPGW N+RHC TGL G D G R ++ PLA Sbjct: 301 LDYVTGEVITALKADVPVEGVCLYPILDYPGWANDRHCETGLYGLCDEDGGRCLYQPLAA 360 Query: 361 ELTLQRRR 368 L + R Sbjct: 361 ALERAQAR 368 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: 496 Number of extensions: 14 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: 389 Length of database: 387 Length adjustment: 30 Effective length of query: 359 Effective length of database: 357 Effective search space: 128163 Effective search space used: 128163 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: 50 (23.9 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