Align beta-fructosidase for D-raffinose catabolism (EC 3.2.1.26) (characterized)
to candidate Ga0059261_1778 Ga0059261_1778 Beta-fructosidases (levanase/invertase)
Query= reanno::Korea:Ga0059261_1778 (502 letters) >FitnessBrowser__Korea:Ga0059261_1778 Length = 502 Score = 1060 bits (2741), Expect = 0.0 Identities = 502/502 (100%), Positives = 502/502 (100%) Query: 1 MKKLAILLTAAAVLASAASAQQADVRPGYHYGPARNWMNDPNGLVYYDGEYHLFYQYNPH 60 MKKLAILLTAAAVLASAASAQQADVRPGYHYGPARNWMNDPNGLVYYDGEYHLFYQYNPH Sbjct: 1 MKKLAILLTAAAVLASAASAQQADVRPGYHYGPARNWMNDPNGLVYYDGEYHLFYQYNPH 60 Query: 61 GDRWGHMNWGHAVSRDLVNWEELPVAIPETDVMAFSGTAVIDWNNTTGFGKNGKPPMIAI 120 GDRWGHMNWGHAVSRDLVNWEELPVAIPETDVMAFSGTAVIDWNNTTGFGKNGKPPMIAI Sbjct: 61 GDRWGHMNWGHAVSRDLVNWEELPVAIPETDVMAFSGTAVIDWNNTTGFGKNGKPPMIAI 120 Query: 121 YTGHDPKTERQSQYLAYSNDRGRTFTIHGEVLNAGNEKHFRDPKVFWHAPTRRWVMVVLK 180 YTGHDPKTERQSQYLAYSNDRGRTFTIHGEVLNAGNEKHFRDPKVFWHAPTRRWVMVVLK Sbjct: 121 YTGHDPKTERQSQYLAYSNDRGRTFTIHGEVLNAGNEKHFRDPKVFWHAPTRRWVMVVLK 180 Query: 181 AAANTAEIYTSPNLKDWTHRSSFGPAGGRGKFWECPDLFELPVEGGAPGETRWVLSINLG 240 AAANTAEIYTSPNLKDWTHRSSFGPAGGRGKFWECPDLFELPVEGGAPGETRWVLSINLG Sbjct: 181 AAANTAEIYTSPNLKDWTHRSSFGPAGGRGKFWECPDLFELPVEGGAPGETRWVLSINLG 240 Query: 241 DNAIGGGSGGQYFVGDFDGEKFTLVPGWPAAPQWMDYGADFYATISWNDMPKGDPRRVWM 300 DNAIGGGSGGQYFVGDFDGEKFTLVPGWPAAPQWMDYGADFYATISWNDMPKGDPRRVWM Sbjct: 241 DNAIGGGSGGQYFVGDFDGEKFTLVPGWPAAPQWMDYGADFYATISWNDMPKGDPRRVWM 300 Query: 301 GWANDWRYAEAIPTWPARGIMTVARTVALRKTAEGYHLLQAPVRELATLRGTPQRAPALA 360 GWANDWRYAEAIPTWPARGIMTVARTVALRKTAEGYHLLQAPVRELATLRGTPQRAPALA Sbjct: 301 GWANDWRYAEAIPTWPARGIMTVARTVALRKTAEGYHLLQAPVRELATLRGTPQRAPALA 360 Query: 361 LSETPVPLPIEGGKADIELELDTGTADQVSIALTDGQGWQTRIGVNPTVNEVFVDRTRSG 420 LSETPVPLPIEGGKADIELELDTGTADQVSIALTDGQGWQTRIGVNPTVNEVFVDRTRSG Sbjct: 361 LSETPVPLPIEGGKADIELELDTGTADQVSIALTDGQGWQTRIGVNPTVNEVFVDRTRSG 420 Query: 421 PHFHDGFANRHVAPVDLKSRKVKLRVLADESIVEVFVNDGRQTITDRFYRGGGALTWSAT 480 PHFHDGFANRHVAPVDLKSRKVKLRVLADESIVEVFVNDGRQTITDRFYRGGGALTWSAT Sbjct: 421 PHFHDGFANRHVAPVDLKSRKVKLRVLADESIVEVFVNDGRQTITDRFYRGGGALTWSAT 480 Query: 481 ARGGKATMNLTAWPMRSMESRK 502 ARGGKATMNLTAWPMRSMESRK Sbjct: 481 ARGGKATMNLTAWPMRSMESRK 502 Lambda K H 0.318 0.135 0.441 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: 1359 Number of extensions: 49 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: 502 Length of database: 502 Length adjustment: 34 Effective length of query: 468 Effective length of database: 468 Effective search space: 219024 Effective search space used: 219024 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 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