Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate 7024753 Shewana3_1931 alpha-glucosidase (RefSeq)
Query= CAZy::AEW20125.1 (708 letters) >FitnessBrowser__ANA3:7024753 Length = 703 Score = 506 bits (1303), Expect = e-147 Identities = 284/706 (40%), Positives = 402/706 (56%), Gaps = 66/706 (9%) Query: 17 LVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEIEGFS-LR 75 L+ T + L SPD +++ + G P Y++ + K +I+PSRLGL L Sbjct: 39 LLCTSATAQTLNLSSPDKQIVLSLS-DDTGRPEYQIHFHGKSIIEPSRLGLVFASLGELG 97 Query: 76 KAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDDGLGF 135 + +K + + DE W WGE + I++ +N+++ L DG + + F+ +DDG+GF Sbjct: 98 QGLRIKSSHSASADEQWQQPWGEQEWIKDQHNQLSVVL--TDGKIDLNLEFKAFDDGIGF 155 Query: 136 RYEFPQQKSL---NYFVIKEEYSEFAMAGDHKA--FWIPG-DYDTQEYDYTESRLTEIRG 189 RY Q +L I +E +EF + KA +WIP ++ EY Y S L ++ Sbjct: 156 RYHLAAQHALPNNTPLAITDELTEFNIGQSDKATAWWIPSRGWNRYEYLYRTSALNQV-- 213 Query: 190 LMQTAITPNTSQTPFSPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQS 249 + + TPF+ K DG ++++HEAALVD+ M+L+ + ++ Sbjct: 214 --------DRAHTPFT---------FKLVDGTHLSIHEAALVDFASMTLD-QQRDGKLKA 255 Query: 250 WLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVKYI 309 LTP + G + Q +TPWRT+ ++D A +L SHL LNLNEP KL DVSW++P KY+ Sbjct: 256 DLTPWSDGIRVKTQAGFYTPWRTIQIADKATGLLNSHLILNLNEPNKLGDVSWVKPGKYV 315 Query: 310 GVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQV 369 G+WW M ++TW TH A + RY+DFAAK+ FD V Sbjct: 316 GIWWGMHLNENTWG-------------------SGPTHGATTSETERYMDFAAKYQFDGV 356 Query: 370 LVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRNY 428 LVEGWN GW+ DWF N F F Y DFDL A+ Y KGV+L+ HHET+ SV +Y Sbjct: 357 LVEGWNQGWDGDWFHNGDQ--FSFTKAYDDFDLPAITAYGAKKGVRLIGHHETAGSVTHY 414 Query: 429 ERQMEKAYKLMNDYGYNAVKSGYVG----------NIIPRGEYHYGQWMVNHYLYAVKKA 478 QM+ A+ L +G VK+GYV N I R E+H GQ+MV YL++V +A Sbjct: 415 RNQMDDAFALYEKHGVTQVKTGYVADGGQIKRIDENGITRHEWHDGQFMVGEYLHSVTEA 474 Query: 479 AEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTRLMGG 536 A+H I +N+HE ++ TGL RTYPN + E ARG EY ++G N HT +LPFTR++ G Sbjct: 475 AKHHISINSHEPIKDTGLRRTYPNWLAREGARGQEYNAWGSPPNNPEHTAMLPFTRMLAG 534 Query: 537 PMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDAFQ 596 PMD+TPGIF+ + ++ N V +TL +QLALYV +YSP+QMAADLP NY++ +DAFQ Sbjct: 535 PMDFTPGIFDLAPKGLDAENR--VQTTLMKQLALYVVLYSPIQMAADLPRNYQKHLDAFQ 592 Query: 597 FIKDVAIDWDDSKYLEAEPGRYITVARKAKGTNNWFVGCTANEDGHLSNVSLDFLDPGRK 656 FI+DV DW S L E G Y+ AR+AK +W++G +E+ V LDFLDP ++ Sbjct: 593 FIRDVPTDWYQSIALAGEVGDYVVFARQAKDQQDWYLGALTDENTREVKVKLDFLDPNKR 652 Query: 657 YTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAI 702 Y A IY D A ++ NP Y I+ +V K LTL+ AS GG AI Sbjct: 653 YQAQIYRDGAKADWKTNPYDYVIETKEVNAKDSLTLQLASSGGTAI 698 Lambda K H 0.319 0.135 0.417 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: 1471 Number of extensions: 82 Number of successful extensions: 10 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: 708 Length of database: 703 Length adjustment: 39 Effective length of query: 669 Effective length of database: 664 Effective search space: 444216 Effective search space used: 444216 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 (21.7 bits) S2: 54 (25.4 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