Align sucrose-6-phosphate hydrolase (ScrB) (EC 3.2.1.26) (characterized)
to candidate CA265_RS18440 CA265_RS18440 glycoside hydrolase
Query= CAZy::CAG25843.1 (469 letters) >FitnessBrowser__Pedo557:CA265_RS18440 Length = 506 Score = 111 bits (278), Expect = 5e-29 Identities = 130/484 (26%), Positives = 197/484 (40%), Gaps = 95/484 (19%) Query: 28 PCWHLAPVTGLMNDPNGFCWSGGRYHLFYQWNPLACDHKYKCWGHWSSTDLLHWQHEPLA 87 P +H + +NDPNG + G +HL+YQ+NP + WGH +S DL++W+H P+A Sbjct: 29 PTYHFTAPSNWLNDPNGLIYLNGEFHLYYQYNPFENKWGHMSWGHATSKDLVNWKHLPVA 88 Query: 88 LMPDK--EYDRNGCYSGSAV----------NNQGVLTLCYTGNVKFDDGSRTAWQCLATE 135 + P+K + +SGSAV + + YT ++ R Q +A Sbjct: 89 I-PEKITKDTTTMIFSGSAVLDKRNVSGLGKGKAPVVAFYTADL---PKQRNESQYMAYS 144 Query: 136 NNQGGFDKLGPVIPLPDGYTGHVRDPKVWKHNS--QWYMVLGAQDKEKRGKVLLYSSVDL 193 N+ G P+ D RDP VW H S QW M + D+ + Y S +L Sbjct: 145 NDGGLSFTNYAKNPIIDLNKKDFRDPNVWWHESTQQWIMTVAMVDEH---QARFYGSKNL 201 Query: 194 YTWSFHGEIAGNGLNEIDNAGYMWECPDF--FALDGE--------YILLCCPQGMVREHE 243 W+ + G N G WECP A+DG I L P+G + Sbjct: 202 KDWTMLSDFGKQG-----NQGSGWECPFIIPLAVDGNKDNTKWVLAISLFGPKGPTMQ-- 254 Query: 244 RYLNTYPCAWLHGQFDYETGKFTHGAFSEL--DAGFEFYAP-QTMEAPDGRRLLVGWMGV 300 + G FD +T K + L D G FYA +AP +R+L+GW+ Sbjct: 255 ---------YFVGDFDGKTFKNDNDGKLTLLVDEGDSFYAAIPWNDAPKRQRILLGWL-Q 304 Query: 301 PDGEEMLQPTRKHHWQHQMTCFRELSFQQG----KLFQMPIRELA--------------- 341 P G+E W+ QM+ R+L+ + +LFQ P + Sbjct: 305 PGGKETFP------WKGQMSIPRDLALKTTPEGIRLFQQPASLIGDNMKKHSGGKVITRQ 358 Query: 342 QLREAEHFWQGKADHAPHVEIERLEMDIIPSG----ELYLNFGNAL-ALHLNDDGIQLQ- 395 L +H G + ++ ++ E D G +L GN + + + D I+ Q Sbjct: 359 NLIIDQHIDLGTSQNSYWIDAEFSVSDAEKIGFKLAQLKDEKGNVVKEVEVGYDAIKKQL 418 Query: 396 ----RRSLAG--------QEKLTRYWRGSVTSLKILCDSSSVEIFINNGEGVMSNRYFPH 443 RS G Q G + L++L D SS+E+F N GE V+S FP Sbjct: 419 YVDCTRSEKGIKNDKNIIQTAAVNSVNGKI-KLQVLFDKSSLEVFGNAGEKVISTMIFPD 477 Query: 444 HPAS 447 A+ Sbjct: 478 EKAT 481 Lambda K H 0.321 0.138 0.463 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: 727 Number of extensions: 49 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 469 Length of database: 506 Length adjustment: 34 Effective length of query: 435 Effective length of database: 472 Effective search space: 205320 Effective search space used: 205320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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