Align Alpha,alpha-phosphotrehalase (EC 3.2.1.93) (characterized)
to candidate AZOBR_RS09450 AZOBR_RS09450 alpha-amylase
Query= reanno::pseudo3_N2E3:AO353_15985 (549 letters) >FitnessBrowser__azobra:AZOBR_RS09450 Length = 1107 Score = 216 bits (549), Expect = 5e-60 Identities = 169/552 (30%), Positives = 260/552 (47%), Gaps = 99/552 (17%) Query: 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNGYDI 63 ++ +VIYQ++ K+F + GD+ G+ KLDY+Q LGV LW+ PF SP RD+GYDI Sbjct: 17 YKDAVIYQLHVKAFFDADNDGIGDIAGLTQKLDYIQELGVTTLWLLPFYPSPLRDDGYDI 76 Query: 64 SDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSL-DNPYRD 122 +DY A++PSYG + D + + E RG++++ ++V+NHTS +H WFQ+AR + + +R+ Sbjct: 77 ADYKAVNPSYGNLQDFKRFLRECHDRGLRVITELVINHTSDQHPWFQRARQAKPGSNHRN 136 Query: 123 FYIWRDQPNNWES------KFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFK 176 FY+W D ++ S W ++++ YF H F Q DLN+DNP+V EV Sbjct: 137 FYVWSDTDQKYQGTRIIFCDTEKSNWTWDSEAQAYFWHRFYSHQPDLNFDNPKVLQEVLN 196 Query: 177 LMRFWRDKGVGGFRLDVINLISKPADFPEDHTDGRRFYTDGPNVHEYLQEMHREVFEGH- 235 +MRFW D GV G RLD + + + + T+ P H+ L+ + E+ +G+ Sbjct: 197 VMRFWLDMGVDGLRLDAVPYLKE-----REGTNNENL----PETHDVLKAIRTEIDKGYG 247 Query: 236 DLINVGEMSSTSLEHCIRYSRPDSK---ELSMTFNFHHLKVDYPNMQKWVRADFDFLELK 292 D + + E + E + Y K E M F+F + Y M + ++ Sbjct: 248 DRMLLAEANQWP-EDVLPYFGDLEKGGDECHMAFHFPLMPRIY--MAVAMEDRHPIADIM 304 Query: 293 RILSDWQTGMQAGGGWNALFWCNHDQ---PRVVSR--------FGDDGEHRV-------- 333 R D Q W A+F NHD+ V R + D R+ Sbjct: 305 RQTPDIPDECQ----W-AIFLRNHDELTLEMVTDRERDYLWDFYAADRRMRINLGIRRRL 359 Query: 334 --------VSAKMLGTALHFLQGTPFIYQGEELGMTNPGFERIEQYRDVETLNIYRLKRE 385 ++L + L + GTP +Y G+E+GM + NIY Sbjct: 360 APLLQNDRRKIELLKSLLLSMPGTPVLYYGDEIGMGD---------------NIY----- 399 Query: 386 AGESEASSMAAIMQKSRDNSRTPMQWSALPNAGFSSSEP-WIGVPA------NAMQINVE 438 RD RTPMQWS N GFS ++P + +PA INVE Sbjct: 400 -------------LGDRDGVRTPMQWSPDRNGGFSRADPARLYLPAIQDPIYGFQAINVE 446 Query: 439 NQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQLLPTHKQVWVYLR----EGEGERLLVV 494 Q +S+L+ ++LIA+R+ G ++ L P +++V YLR E E +L V Sbjct: 447 AQQRSPSSLLNWMKRLIAVRQQHKAFGRGRFQLLYPGNRKVLAYLRCHSTEEGDEVILCV 506 Query: 495 NNFYGTACEVEL 506 N +A VEL Sbjct: 507 ANLSRSAQAVEL 518 Lambda K H 0.321 0.137 0.436 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: 1637 Number of extensions: 81 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 549 Length of database: 1107 Length adjustment: 41 Effective length of query: 508 Effective length of database: 1066 Effective search space: 541528 Effective search space used: 541528 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 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