Align α-glucosidase / binding-toxin receptor (Agm3;AgAgm3) (EC 3.2.1.20) (characterized)
to candidate WP_013429333.1 CALKRO_RS01320 alpha-amylase
Query= CAZy::ABW98683.1 (588 letters) >NCBI__GCF_000166775.1:WP_013429333.1 Length = 514 Score = 215 bits (547), Expect = 4e-60 Identities = 157/497 (31%), Positives = 244/497 (49%), Gaps = 61/497 (12%) Query: 41 FYQIYPRSFQDSNGDGIGDLKGITARMEYLAGLGIDATWLSPPFVSPLADFGYDVADFYD 100 FY+++ RSF DSNGDGIGD+ G+ ++ Y+ LG++A WL P F SP + GYDV ++Y Sbjct: 42 FYEVFVRSFYDSNGDGIGDINGLAEKLPYIKSLGVNAIWLMPIFESP-SYHGYDVTNYYK 100 Query: 101 IQPEYGTLADMEELIAEAHRHGIKLMLDFIPNHSSDEHDWFVQ-SANGVAKYRDYYIWRP 159 + P+YGT D I +AH+ GIK+++D + NH+S +H WF++ S+N +KYR+YYIW Sbjct: 101 VNPDYGTNEDFVNFIKKAHKMGIKVIIDMMINHTSSKHPWFIEASSNKNSKYRNYYIWAT 160 Query: 160 GRQNSQTGALEPPNNWISVFGGPAWTYDERRGEFYLHQ-FTKKQADLNYRNPAVVEEMTK 218 N L+ P S G W ++G+ Y + F + DLN+ N AV EEM K Sbjct: 161 PNTN-----LDEP----SELGTRQW---YKKGDSYYNAIFWSEMPDLNFDNKAVREEMKK 208 Query: 219 MLSFWLEKGVDGFRLDAINHMFEDAQLRDEPPGWGAPGTYDELDHIYTKDNPDTYNVVYG 278 + FWLEKGVDGFRLDA H++ ++ +D W +E D Y V Sbjct: 209 IAKFWLEKGVDGFRLDAAKHIYPLSREKDTLVWW------EEYAKFCRSIKKDVYLVAEV 262 Query: 279 WRQLCDDFGRRMNKTIIIMTEAYASIENTMLYYEDATGTRQGAHMPFNFQLIYDFRHD-Q 337 W L +R+ + YA I ++ + A +G +IY+ Q Sbjct: 263 WDSL-----QRIAQ--------YAKIFDSCFNFIIAQNIIEG--------VIYENTQTLQ 301 Query: 338 NAIGLKQSIDFWLNHMPARHTASWVAGSHDHSRVGSRVGL-EHVDQVLTLLHTLPGTSIT 396 N L + + N P A ++ +HD +R + +G + LL TLPG Sbjct: 302 N--NLSSIYNLYKNVNPQFVDAPFLT-NHDMNRAYTEIGSNSKMKLAAALLLTLPGNPFI 358 Query: 397 YYGEEIGMLDFKDAQLYDNRDPNRTPMQWDNSISAGFSTNRTTWLRLHPDYPTRNVAMQE 456 YYGEEIGM K + R P +W + G + + PD +V QE Sbjct: 359 YYGEEIGMKGQKPDEYI------REPFKWYETWKKGQTNWEMSLYNSGPD--VASVEKQE 410 Query: 457 AAEKSTLKHFRTLTALR-RHPTLVHGEFKHRTVGPDVYAFSRELHGEDTLVTVLNMATSS 515 + S L +R + + R ++ L+ G+F+ D+ +F+R ++ +V + N Sbjct: 411 KDKNSLLNFYRDMISFRKKNLPLLKGDFQLIKTSFDILSFAR-VYNNQKMVVIFNFTGK- 468 Query: 516 RTVDLGDFVNLPARLTV 532 +L +NLP+ + + Sbjct: 469 ---ELSKTINLPSNINI 482 Lambda K H 0.320 0.136 0.423 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: 788 Number of extensions: 46 Number of successful extensions: 6 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: 588 Length of database: 514 Length adjustment: 36 Effective length of query: 552 Effective length of database: 478 Effective search space: 263856 Effective search space used: 263856 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 (21.8 bits) S2: 53 (25.0 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