Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__Keio:1937187 Length = 833 Score = 356 bits (914), Expect = e-102 Identities = 237/694 (34%), Positives = 365/694 (52%), Gaps = 40/694 (5%) Query: 179 PNGLHARPAAVFAQAAKGFAASICLH--KQQDSANAKSLVAIMALQTVHGDALQVSAVGE 236 PNG+HARPA+ F++ I H + NAKS +A++ T+ GD Q+ G Sbjct: 12 PNGVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGA 71 Query: 237 DAELAISTLAQLLADGCGEAVTPVAVVAP------VVEAQEVSTKLLRGVCASAGSAFGY 290 D + A L+Q L D P+A V V ++ +++R +GSA G Sbjct: 72 DEQEAHQRLSQWLRDEFPHCDAPLAEVKSDELEPLPVSLTNLNPQIIRARTVCSGSAGGI 131 Query: 291 VVQVAERTLE----MPEFAADQQLERESLERALMHATQALQ-RLRDNAAGEAQADIFKAH 345 + ++ L +P A E+ +LE L + ++ RL D+ A + I +AH Sbjct: 132 LTPISSLDLNALGNLPA-AKGVDAEQSALENGLTLVLKNIEFRLLDSDG--ATSAILEAH 188 Query: 346 QELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRV 405 + L D SL E A ++ G S A A ++ F S+ L ERALD+ DV ++ Sbjct: 189 RSLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSSYLQERALDVRDVCFQL 248 Query: 406 LKLILGVP--DGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARA 463 L+ I G +L AI +A++LTPSQ LD + G GG TSH ILAR+ Sbjct: 249 LQQIYGEQRFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLLLKSGGTTSHTVILARS 308 Query: 464 LGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELEN 523 +P + G+ + L+ + +D + G + ++P +V A+ QQ R Q L Sbjct: 309 FNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAV-----ARYYQQEARVQDALRE 363 Query: 524 AARA-----AVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHD 578 R A T DG E+ AN+A E + A GAEG+GL R+E LY R+ AP Sbjct: 364 QQRVWLTQQARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFRTEMLYMDRTSAPGES 423 Query: 579 EQAGTY-SAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQL 637 E + A+ A G R+++VRT+D+GGDKP+ Y+ + +EANPFLG R +R+ E L Sbjct: 424 ELYNIFCQALESANG--RSIIVRTMDIGGDKPVDYLNIPAEANPFLGYRAVRIYEEYASL 481 Query: 638 LREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELP-----KLGIM 692 Q R+IL ++ L IM+PM+S + E+ + L E L +P +LGIM Sbjct: 482 FTTQLRSILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNEHIPFDEKIQLGIM 541 Query: 693 IEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTV 752 +EVP+ + D E+DFFSIG+NDLTQY LA+DRD+ ++ +S +P+ LR + V Sbjct: 542 LEVPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAV 601 Query: 753 KAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIA 812 +A H GKW+G+CG L ++ +PLL+GLG+DELS+S P IPA KA + +++ +C+ + Sbjct: 602 QAVHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKARMAQLDSRECRKLL 661 Query: 813 HQVLGLESAEQVREALS----VQQQAMVETSQVL 842 +Q + ++ +V L+ QQ A + T++ + Sbjct: 662 NQAMACRTSLEVEHLLAQFRMTQQDAPLVTAECI 695 Lambda K H 0.318 0.132 0.370 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: 1240 Number of extensions: 53 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: 844 Length of database: 833 Length adjustment: 42 Effective length of query: 802 Effective length of database: 791 Effective search space: 634382 Effective search space used: 634382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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