Align β-galactosidase (BgalH) (EC 3.2.1.23) (characterized)
to candidate GFF72 Psest_0072 hypothetical protein
Query= CAZy::AFA35120.1 (389 letters) >FitnessBrowser__psRCH2:GFF72 Length = 384 Score = 495 bits (1274), Expect = e-144 Identities = 232/372 (62%), Positives = 283/372 (76%), Gaps = 1/372 (0%) Query: 1 MHQPSLFKSFFLGGFECSTHRRRDGRRLDLIAGTRHDQYASNDYAALAHHAIHSVRDGMR 60 MH PSLFKSFFLGGFECS HRR DGRRLDLIA T HD++A++DYA L + + SVRDG+R Sbjct: 1 MHHPSLFKSFFLGGFECSNHRRSDGRRLDLIAATGHDRWAAHDYAELHRYGLRSVRDGLR 60 Query: 61 WHLIETAKGRYDWSSVLPMIRAAKAQRTEVIWDLCHYGWPDDIDIFKAEFVERFAAYAAA 120 WHLIE G+YDWSS LPM++AA+ Q T+VIWDLCHYGWPDDIDI++ +FVERFA YAAA Sbjct: 61 WHLIERQPGQYDWSSFLPMLQAAQRQGTQVIWDLCHYGWPDDIDIWRPQFVERFARYAAA 120 Query: 121 ATRLLRNEGIEAPLITPLNEISFWAWAGGSVAHFNPTVRRRGDELKRQLVRAAIAAMEAI 180 A +L+++E E P PLNEISFWAWAGG A+FNP R RG ELK QLVRA IAAM+AI Sbjct: 121 AAQLIKDETGEVPFYAPLNEISFWAWAGGDEAYFNPMARGRGFELKHQLVRATIAAMQAI 180 Query: 181 REILPKARFIQVDPIIHVVSRSTRRRDRERAERLKFEQYTAWDMLCGAQHPELGGKPAYL 240 R + P+ARF+QVDP IHVV+ + R + AER + Q+ AWDMLCG Q P LGG P YL Sbjct: 181 RAVEPRARFVQVDPAIHVVAANDRPGPQRDAERFRQSQFEAWDMLCGEQWPGLGGAPEYL 240 Query: 241 DIMGVNYYPHNQWY-ANRQDIPMDSPDYRPFHKLLADAFQRYGKPLLIAETGAESERRVP 299 D++G+NYY +NQWY + + I D+PDYRPF +L + QRY +PLLIAETGAE + R Sbjct: 241 DVLGINYYSNNQWYHGDGRTIERDNPDYRPFKGILREIHQRYQRPLLIAETGAEGDVRGD 300 Query: 300 WVRYVCEQVDIALRQNIPVEGICLYPITDYPGWENNRHCRTGLLGYADAQGQRPVFSPLA 359 W+RYV EQ +A++ +PVEGICLYP+ DYPGW + RHC GLLG+ D G+R V LA Sbjct: 301 WLRYVSEQAGLAMQAGVPVEGICLYPVLDYPGWTDERHCPVGLLGFPDEIGKRCVHEGLA 360 Query: 360 DELTLQRRRFER 371 DEL LQ+ RF + Sbjct: 361 DELRLQQMRFSQ 372 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: 533 Number of extensions: 20 Number of successful extensions: 2 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: 384 Length adjustment: 30 Effective length of query: 359 Effective length of database: 354 Effective search space: 127086 Effective search space used: 127086 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