Align fructan beta-fructosidase (EC 3.2.1.80) (characterized)
to candidate CA265_RS18440 CA265_RS18440 glycoside hydrolase
Query= BRENDA::P05656 (677 letters) >FitnessBrowser__Pedo557:CA265_RS18440 Length = 506 Score = 374 bits (959), Expect = e-108 Identities = 221/526 (42%), Positives = 304/526 (57%), Gaps = 49/526 (9%) Query: 11 MFTLLLTMAFSADAADSSYYDE---DYRPQYHFTPEANWMNDPNGMVYYAGEYHLFYQYH 67 MF +AF + S++ + +RP YHFT +NW+NDPNG++Y GE+HL+YQY+ Sbjct: 1 MFKTKYILAFLMCCSISTFAQQPTPQWRPTYHFTAPSNWLNDPNGLIYLNGEFHLYYQYN 60 Query: 68 PYGLQWGPMHWGHAVSKDLVTWEHLPVA----LYPDEKGTIFSGSAVVDKNNTSGFQTGK 123 P+ +WG M WGHA SKDLV W+HLPVA + D IFSGSAV+DK N SG GK Sbjct: 61 PFENKWGHMSWGHATSKDLVNWKHLPVAIPEKITKDTTTMIFSGSAVLDKRNVSGLGKGK 120 Query: 124 EKPLVAIYTQD--REGHQVQSIAYSNDKGRTWTKYAGNPVIPNPGKKDFRDPKVFWYEKE 181 P+VA YT D ++ ++ Q +AYSND G ++T YA NP+I + KKDFRDP V+W+E Sbjct: 121 -APVVAFYTADLPKQRNESQYMAYSNDGGLSFTNYAKNPII-DLNKKDFRDPNVWWHEST 178 Query: 182 KKWVMVLAAGD--RILIYTSKNLKQWTYASEFGQDQGSHGGVWECPDLFELPVDGNPNQK 239 ++W+M +A D + Y SKNLK WT S+FG+ QG+ G WECP + L VDGN + Sbjct: 179 QQWIMTVAMVDEHQARFYGSKNLKDWTMLSDFGK-QGNQGSGWECPFIIPLAVDGNKDNT 237 Query: 240 KWVMQVSVGNGAVSGGSGMQYFVGDFDGTHFKNENPPNKVLWTDYGRDFYAAVSWSDIPS 299 KWV+ +S+ G MQYFVGDFDG FKN+N L D G FYAA+ W+D P Sbjct: 238 KWVLAISLFG---PKGPTMQYFVGDFDGKTFKNDNDGKLTLLVDEGDSFYAAIPWNDAPK 294 Query: 300 TDSRRLWLGWMSNWQYANDVPTSPWRSATSIPRELKLKAFTEGVRVVQTPVKELETIRGT 359 +R+ LGW+ T PW+ SIPR+L LK EG+R+ Q P + Sbjct: 295 --RQRILLGWLQ----PGGKETFPWKGQMSIPRDLALKTTPEGIRLFQQPASLIGDNMKK 348 Query: 360 SKKWKNLTISP--ASHNVLAGQSGDAYEINAEFKVSPGSAAEFGFKVRTGENQ------F 411 K +T ++ G S ++Y I+AEF VS A + GFK+ +++ Sbjct: 349 HSGGKVITRQNLIIDQHIDLGTSQNSYWIDAEFSVS--DAEKIGFKLAQLKDEKGNVVKE 406 Query: 412 TKVGYDRRNAKLFVD--RSESG--NDTFNPAFNTGKETAPLKPVNGKVKLRIFVDRSSVE 467 +VGYD +L+VD RSE G ND +TA + VNGK+KL++ D+SS+E Sbjct: 407 VEVGYDAIKKQLYVDCTRSEKGIKND------KNIIQTAAVNSVNGKIKLQVLFDKSSLE 460 Query: 468 VFGNDGKQVITDIILPDRSSKGLELYAANGGVKVKSLTIHPLKKVW 513 VFGN G++VI+ +I PD + GL ++ G + L KVW Sbjct: 461 VFGNAGEKVISTMIFPDEKATGLAAFSNGGKAVLNKL------KVW 500 Lambda K H 0.316 0.134 0.414 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: 1139 Number of extensions: 70 Number of successful extensions: 9 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: 677 Length of database: 506 Length adjustment: 37 Effective length of query: 640 Effective length of database: 469 Effective search space: 300160 Effective search space used: 300160 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 (21.6 bits) S2: 53 (25.0 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