Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate WP_013429617.1 CALKRO_RS02895 alpha-xylosidase
Query= CAZy::AAO75446.1 (748 letters) >NCBI__GCF_000166775.1:WP_013429617.1 Length = 759 Score = 764 bits (1972), Expect = 0.0 Identities = 349/749 (46%), Positives = 510/749 (68%), Gaps = 5/749 (0%) Query: 1 MKPTNYHLFDFLDFDTELLRDESLWKACKPTAVYEK-DGDICVTVPFQKQLLANDMVADT 59 MK N +D LDFD +++ LW A VYE+ DG + + +PFQ Q V D Sbjct: 1 MKQKNSFKYDMLDFDLPEAKNDILWIAEMAEEVYEQSDGSVIIKIPFQAQK-KEVFVPDN 59 Query: 60 AVPREEYTLIIRQYNIGITRLFLGFGEYELTDQSE-MLQFSERIRRVPLSVEKQGGKWIL 118 + ++ Y + ++ Y+ I R + FG + D + M++++ +++ L V K W + Sbjct: 60 SKEKKYYYMEVKAYDDAIVRCSISFGGKFMEDNNNPMIEWAPSLKQEKLYVIKNKNGWDI 119 Query: 119 FTQDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGL 178 + R +N + + +WS L P+PQ + ++PDG + A D F+P + + Sbjct: 120 VDDNKVVRMKVNNIKKPVRKWSNLHPEPQYFFNAKIFPDGIIAVSFLANDTFTPGIVESV 179 Query: 179 PIAFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYK 238 + + + GK +R + S +E FAGTGERF M+L+G+T+ L+N D GVNNRR YK Sbjct: 180 SLGYVEHDGKADRCVFALHSEYNEKFAGTGERFAPMNLAGKTIILENNDALGVNNRRAYK 239 Query: 239 NIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYR 298 N+PFY+SS+ YG T AH +LSLA STR+VQ L + +LD F I G E I+ YR Sbjct: 240 NVPFYISSKGYGLLIMTSAHVRLSLADISTRAVQALIEDDVLDLFFIGGGEPERIIYNYR 299 Query: 299 DLTGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCE 358 +TG+P P WS+G+WMSRM+YFSA+E ++ ++R +PCDVIHLDTGWF+ DW C+ Sbjct: 300 RITGFPRKVPAWSYGIWMSRMSYFSAEETLDVAKKLRENGFPCDVIHLDTGWFKKDWQCD 359 Query: 359 WKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDG 418 W+F+EERFP+P+ +I+ + K G+++S+WQLP VA + + A N++I+ +TK + Sbjct: 360 WEFDEERFPNPQEYIKNMHKMGFKISVWQLPQVAAETKHYNVAIENKFISRITKMSEEST 419 Query: 419 SNFSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELL 478 SNF ++Y G IDFT PKA +WY+ LLK L D+GV IKTDFGENI M+A Y M+P+ L Sbjct: 420 SNFGDVEYRGVIDFTNPKAVKWYQNLLKNLFDLGVDVIKTDFGENIDMNAEYFSMEPKKL 479 Query: 479 NNLYALLYQKAAYEITKEVTGDG--IVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKG 536 +N+Y+LLYQKAA+EIT+EV G G I+WARA W GCQRYP+HWGGDS S+WDG+A +++G Sbjct: 480 HNIYSLLYQKAAFEITEEVKGKGQAIIWARAGWIGCQRYPVHWGGDSSSTWDGLAATIRG 539 Query: 537 GLHFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWH 596 GLH G+SGF FWSHDVPGFH LP+FMN+ +D+Y+RWTQ VFTSHIRYHGT+ REP++ Sbjct: 540 GLHLGVSGFGFWSHDVPGFHGLPDFMNNWPDDDIYVRWTQVAVFTSHIRYHGTSPREPYN 599 Query: 597 YPAIAPLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFG 656 YP ++ ++++WWKLRY+LIPY +EQ + ++G+P ++AL++HHP+D+ CW+IDDE+Y G Sbjct: 600 YPNVSDIIREWWKLRYALIPYFVEQGEKVTKTGYPFIRALLIHHPDDEYCWYIDDEFYCG 659 Query: 657 NDFLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIP 716 + FLVAP++NS +R+IYLP+G W++F++GE ++G LK+VY PLE +P+Y + + Sbjct: 660 DIFLVAPIINSAGKRNIYLPKGNWIDFWSGEFIKGPILLKDVYFPLERIPIYCVAGSELK 719 Query: 717 IYPEEVNCTDEMDLGKSIALRIDHNYKGF 745 +YP V T E++ K+ + DH Y+GF Sbjct: 720 VYPYVVQHTGEIEFDKTKIIVFDHTYRGF 748 Lambda K H 0.322 0.139 0.449 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: 1774 Number of extensions: 80 Number of successful extensions: 4 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: 748 Length of database: 759 Length adjustment: 40 Effective length of query: 708 Effective length of database: 719 Effective search space: 509052 Effective search space used: 509052 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: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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