Align Trehalase; Alpha,alpha-trehalase; Alpha,alpha-trehalose glucohydrolase; EC 3.2.1.28 (characterized)
to candidate H281DRAFT_00297 H281DRAFT_00297 Glucoamylase (glucan-1,4-alpha-glucosidase), GH15 family
Query= SwissProt::P71741 (680 letters) >FitnessBrowser__Burk376:H281DRAFT_00297 Length = 640 Score = 372 bits (956), Expect = e-107 Identities = 241/647 (37%), Positives = 343/647 (53%), Gaps = 43/647 (6%) Query: 43 SSSPLRNPFP-PIADYAFLSDWETTCLISPAGSVEWLCVPRPDSPSVFGAILDR-SAGHF 100 S++ +R P PI DYA + D T LIS GSV+WLC PR DS + F A+L G + Sbjct: 7 SNALIRKLMPAPIEDYALIGDGHTAALISREGSVDWLCWPRFDSGACFAALLGTPDNGRW 66 Query: 101 RLGP-YGVSVPSARRYLPGSLIMETTWQTHTGWLIVRDALVMGK-WHDIERRSRTHRRTP 158 + P V RRY +LI+ET ++T G + + D + G W + Sbjct: 67 LICPDTDAPVKITRRYRGETLILETDFETPEGAVTLVDFMPPGNGWSE------------ 114 Query: 159 MDWDAEHILLRTVRCVSGTVELMMSCEPAFDYHRLGATWEYSAEAYGEAIARANTEPDAH 218 ++R V GTV + M FDY G + + E+ RA PD Sbjct: 115 --------MVRIVVGKRGTVRMKMELVLRFDY---GFSIPWVQRLKNESGIRAIVGPD-- 161 Query: 219 PTLRLTTNLRIGLEGREARARTRMKEGDDVFVALSWT----KHPPPQTYDEAADKMWQTT 274 L T + + E + A +KEG+ V +L++ + PP + A + +T Sbjct: 162 -NAVLRTPVELVGENMKTVAEFTVKEGERVPFSLAYAASHLRLPPARDPHTA---LARTE 217 Query: 275 ECWRQWINIGNFPDHPWRAYLQRSALTLKGLTYSPTGALLAASTTSLPETPRGERNWDYR 334 W +W G+ W ++RS +TL+ L Y PTG ++AA TTSLPE G RNWDYR Sbjct: 218 NHWLEWSARGSIQGR-WAEPIRRSLITLRALAYEPTGGIVAAPTTSLPEQLGGTRNWDYR 276 Query: 335 YAWIRDSTFALWGLYTLGLDREADDFFAFIADVSGANNNERHPLQVMYGVGGERSLVEAE 394 Y W+RD+T L L G EA + +++ V+ ++ LQ+MYG+ GER L E E Sbjct: 277 YCWLRDATITLLALMRGGYYDEARAWRSWLGRVTAGAPDQ---LQIMYGLAGERRLPEFE 333 Query: 395 LHHLSGYDHARPVRIGNGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPVLKRQVEEA 454 + L GY A+PVRIGN A Q Q D++G ++++ +L Q + W V + Sbjct: 334 IDWLPGYQGAKPVRIGNNAVGQLQLDVYGEVMNALHLARVGGLQADDTAWNVQCALLRHL 393 Query: 455 IKHWREPDRGIWEVRGEPQHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKA 514 W++PD GIWE RG QHFT SKVM WVA DR AE + +WRA +I A Sbjct: 394 TTIWQQPDEGIWETRGGRQHFTFSKVMAWVAFDRALASAEMFKLEGPLDEWRATRAQIHA 453 Query: 515 DILEHGVD-SRGVFTQRYGDEALDASLLLVVLTRFLPPDDPRVRNTVLAIADELTEDGLV 573 ++ E + SR F Q YG + LDAS+LL+ L FLPP+DPR++ TV AI +L DG V Sbjct: 454 EVCEKAWNPSRNAFVQAYGSDQLDASVLLMPLVSFLPPNDPRIKGTVEAIERDLMHDGFV 513 Query: 574 LRYRVHETDDGLSGEEGTFTICSFWLVSALVEIGEVGRAKRLCERLLSFASPLLLYAEEI 633 +RYR E DDGL EGTF CSFW+V L G + A + ERLL + + L AEE Sbjct: 514 MRYRTTEFDDGLPPGEGTFLACSFWMVDNLALQGRLDEAIAMYERLLGLCNDVGLLAEEY 573 Query: 634 EPRSGRHLGNFPQAFTHLALINAVVHVIRAEEEADSSGMFQPANAPM 680 +P + R +GNFPQAF+H++L+N +++++ E+A + QP++ M Sbjct: 574 DPAAKRLVGNFPQAFSHVSLVNTGLNLMK-HEQAMARATGQPSHNGM 619 Lambda K H 0.319 0.134 0.425 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: 1349 Number of extensions: 68 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 680 Length of database: 640 Length adjustment: 38 Effective length of query: 642 Effective length of database: 602 Effective search space: 386484 Effective search space used: 386484 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: 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