Align Trehalase; Alpha,alpha-trehalase; Alpha,alpha-trehalose glucohydrolase; EC 3.2.1.28 (characterized)
to candidate PP_4041 PP_4041 putative glycoside hydrolase
Query= SwissProt::P71741 (680 letters) >FitnessBrowser__Putida:PP_4041 Length = 598 Score = 372 bits (955), Expect = e-107 Identities = 234/616 (37%), Positives = 323/616 (52%), Gaps = 37/616 (6%) Query: 54 IADYAFLSDWETTCLISPAGSVEWLCVPRPDSPSVFGAIL-DRSAGHFRLGPYGVSVPSA 112 I DYA L + + L+S G+++WLC+PR D+P+VF A+L + G +RL P S+ Sbjct: 5 IEDYALLGNCRSAALVSRDGALDWLCLPRFDAPAVFAALLGNEENGRWRLAPCDPVTHSS 64 Query: 113 RRYLPGSLIMETTWQTHTGWLIVRDALVMGKWHDIERRSRTHRRTPMDWDAEHILLRTVR 172 R+YL +L++ETTW T +G V D + +G+ + + +R V Sbjct: 65 RQYLGDTLVLETTWVTASGRARVLDFMPLGEVNSV--------------------VRIVE 104 Query: 173 CVSGTVELMMSCEPAFDYHRLGATWEYSAEAYGEAIARANTEPDAHPTLRLTTNLRIGLE 232 +SG M FDY R W E A PD L L + + Sbjct: 105 GLSGETHFEMDLVMRFDYGR-SVPW---VERLDPLTLSAVAGPDR---LILCSTVPPQAR 157 Query: 233 GREARARTRMKEGD-DVFVALSWTKHPPPQTYDEAADKMWQTTECWRQWINIGNFPD-HP 290 R R+ G VF H P Q + T E W+ + + P P Sbjct: 158 DHHTGCRFRVSTGQRQVFSLRHQPSHLPVQPDCNIDQALANTCEQWQAFAD--RCPQVGP 215 Query: 291 WRAYLQRSALTLKGLTYSPTGALLAASTTSLPETPRGERNWDYRYAWIRDSTFALWGLYT 350 + A ++RS LTLK +TY+PTG ++AA TTSLPE GERNWDYR+ W+RD+T L Sbjct: 216 YTALVRRSLLTLKAMTYAPTGGIVAAVTTSLPERVGGERNWDYRFCWLRDATMTLLAFMN 275 Query: 351 LGLDREADDFFAFIADVSGANNNERHPLQVMYGVGGERSLVEAELHHLSGYDHARPVRIG 410 LG EA + ++ S A N E+ +Q+MYG+ GER L E L L+GY+H++PVR+G Sbjct: 276 LGYFDEAQAWREWLLR-SVAGNPEQ--MQIMYGLAGERDLQEYTLPWLAGYEHSQPVRVG 332 Query: 411 NGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPVLKRQVEEAIKHWREPDRGIWEVRG 470 N A QRQ DI+G + D+ K + + + + WREPD GIWEVRG Sbjct: 333 NAASAQRQLDIYGELADAMTQAIKGGLPRHPRSAAISRLILPYVERIWREPDEGIWEVRG 392 Query: 471 EPQHFTSSKVMCWVALDRGAKLAERQGE-KSYAQQWRAIADEIKADILEHGVDSRG-VFT 528 Q F SKVM WVA DR A LA+ E + Q +R +ADEI D+ EHG+D G F Sbjct: 393 GRQQFVHSKVMAWVAFDRAAGLADTTEEGRERGQHYRQVADEIHRDVCEHGLDPSGRFFV 452 Query: 529 QRYGDEALDASLLLVVLTRFLPPDDPRVRNTVLAIADELTEDGLVLRYRVHETDDGLSGE 588 YG +DASLL + LT FLP DDPR T+ I L ++GL+LRY DGL+ Sbjct: 453 HAYGSTEMDASLLQIALTGFLPADDPRFMRTLEQIEQRLMKNGLLLRYDSDSCSDGLTPG 512 Query: 589 EGTFTICSFWLVSALVEIGEVGRAKRLCERLLSFASPLLLYAEEIEPRSGRHLGNFPQAF 648 EGTF +CSFWL V +G +A+ L + L + L L AE+ +P R LGNFPQAF Sbjct: 513 EGTFLVCSFWLADVYVLLGRQAKAEALYQHLTGLCNDLGLLAEQYDPAGQRMLGNFPQAF 572 Query: 649 THLALINAVVHVIRAE 664 + + +IN +++ RA+ Sbjct: 573 SQIGIINTALNLHRAQ 588 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: 1233 Number of extensions: 69 Number of successful extensions: 7 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: 680 Length of database: 598 Length adjustment: 38 Effective length of query: 642 Effective length of database: 560 Effective search space: 359520 Effective search space used: 359520 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