Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate WP_013429624.1 CALKRO_RS02935 glycoside hydrolase family 31 protein
Query= CAZy::AAO75446.1 (748 letters) >NCBI__GCF_000166775.1:WP_013429624.1 Length = 661 Score = 220 bits (560), Expect = 2e-61 Identities = 170/571 (29%), Positives = 272/571 (47%), Gaps = 71/571 (12%) Query: 187 GKKERATLSFESRPDECFAGTGERFFK-MDLSGQTLFLKNQDGQGVNNRRTYKNIPFYLS 245 G R T+ FES P+E G G+ ++L G L L +++ Q ++PF +S Sbjct: 119 GGSYRLTVRFESEPNEKLYGMGQYQQPFLNLKGCALELAHRNSQS--------SVPFLVS 170 Query: 246 SRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDLTGYPS 305 + YG ++ A K+ + T +++ ++D ++ AG+T EIL Y ++TG P Sbjct: 171 NIGYGFLWNNPAIGKVVFGKNITEWEAYVTK--IMDYWITAGNTPAEILEQYMEVTGTPP 228 Query: 306 MPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWKFNEER 365 M P ++ G W S++ Y +A E+ +I + + P DVI +D +F +WKF+E+ Sbjct: 229 MMPDYAMGFWQSKLRYRNAQELMDIAYEYKKRNLPLDVIVID--FFHWPHQGDWKFDEDY 286 Query: 366 FPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYI-----APLTKQQDTDGSN 420 +P P+ ++ L+K G V + P V +++E EE + + P Q + + Sbjct: 287 WPYPEKMVEELRKMGIEVMVSIWPTVEKESENYEEMFSKGLLISTDRGPRVTMQFVNDTL 346 Query: 421 FSALDYAGTIDFTYPKATEWYKGLLKQ-LLDMGVTCIKTDFGE----NIHMDAVYKGMKP 475 F +D T P+A E+ G +K+ G+ D E D + P Sbjct: 347 F--------VDMTNPEAREFMWGKVKENYFSKGIKMYWLDEAEPEFHKYEFDNYRYYLGP 398 Query: 476 EL-LNNLYALLYQKAAYE-ITKEVTGDGIVWARAAWAGCQRY-PLHWGGDSCSSWDGMAG 532 L + N+Y LLY K Y+ + KE + I R AWAG QRY + W GD S+++ + Sbjct: 399 CLEIGNIYPLLYAKTFYDGLKKEGIENIINLIRCAWAGSQRYGVVVWSGDIASTFESLRN 458 Query: 533 SLKGGLHFGLSGFAFWSHDVPGFH----TLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHG 588 + GL+ ++G +W+ D+ GF+ P+F I+ RW QFG F R HG Sbjct: 459 QVACGLNMAMAGIPWWTSDIGGFYGGDPEDPSFRELII------RWFQFGAFCPVFRLHG 512 Query: 589 TNK-------------------REPWHYPAIA-PLVKKWWKLRYSLIPYIIEQSKLAVES 628 K E W Y A + KK+ +R L PYI Q L + Sbjct: 513 DRKPYIPPTSNKGGGRMGSGGPNEVWSYGEEAYEIFKKYLTIREKLKPYIKRQMLLTHKK 572 Query: 629 GWPLLQALILHHPEDKLCWHIDDEYYFGNDFLVAPVMNSENR-RDIYLPEG-QWVNFFTG 686 G P+++ L P D W I+DE+ FG D L+APV+ R R +YLPEG W + TG Sbjct: 573 GTPIMRPLFYDFPFDTKSWEIEDEFMFGPDILLAPVLYEGMRERTVYLPEGAYWREWETG 632 Query: 687 ERLQGGRWLKEV--YVPLEEMPVYVRENAVI 715 + +GG KE+ PL +P+++R+ V+ Sbjct: 633 KVYEGG---KEIICQAPLTTIPIFIRDGVVL 660 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: 1448 Number of extensions: 97 Number of successful extensions: 8 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: 661 Length adjustment: 39 Effective length of query: 709 Effective length of database: 622 Effective search space: 440998 Effective search space used: 440998 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: 54 (25.4 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