Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate 16488 b2383 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >FitnessBrowser__Keio:16488 Length = 831 Score = 330 bits (846), Expect = 2e-94 Identities = 227/677 (33%), Positives = 346/677 (51%), Gaps = 26/677 (3%) Query: 177 PTGLHARPATAWVETARASAARIQ-VRHG-DLVADAKALVALLQLGLRAGDSVVVSAEGD 234 P GLHARPA E + I + H + ADAK+ +AL+ G DS ++ G Sbjct: 11 PNGLHARPAWELKEQCSQWQSEITFINHRQNAKADAKSSLALIGTGTLFNDSCSLNISGS 70 Query: 235 DAVAALARMKATI-TRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIG 293 D A ++ I R + A A R + NP + AS G+ +G Sbjct: 71 DEEQARRVLEEYIQVRFIDSDSVQPTQAELTAHPLPRSLSRLNPDLLYGNVLAS-GVGVG 129 Query: 294 PVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQA 353 + +L ++ + RL +L+ + L R G S+ I +A Sbjct: 130 TLTLLQSDSLDSYRAIPASAQDSTRLEHSLATLAEQLN---QQLRERDGESKT-ILSAHL 185 Query: 354 EILNDTDLVTLACQLMVEGH-GVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRV 412 ++ D + +LM E H G+ + +E+ A L+A + L R +D+RD+ +++ Sbjct: 186 SLIQDDEFAGNIRRLMTEQHQGLGAAIISNMEQVCAKLSASASDYLRERVSDIRDISEQL 245 Query: 413 LARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILAR 472 L P L+ L + P IL+AEDL+PS +LD+ + G+ + G TSHT ILAR Sbjct: 246 LHITWPELKPRNKLVL-EKPTILVAEDLTPSQFLSLDLKNLAGMILEKTGRTSHTLILAR 304 Query: 473 TLGLPAMVAGGAALMELAN--GTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEE 530 +P V G L +A G PA+LD Q G L ++P A + + R+ ++ Sbjct: 305 ASAIP--VLSGLPLDAIARYAGQPAVLDAQCGVLAINPNDAVSGYYQVAQTLADKRQKQQ 362 Query: 531 EARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQ 590 A +RD ++I AN+ + A + GAE VGL RTE L+++R AP E EQ Sbjct: 363 AQAAAQLAYSRDNKRIDIAANIGTALEAPGAFANGAEGVGLFRTEMLYMDRDSAPDEQEQ 422 Query: 591 YETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQ 650 +E Y+ +L A +P+I R +DIGGDK +P+L +P EENPFLG R R+ L TQ Sbjct: 423 FEAYQQVLLAAGDKPIIFRTMDIGGDKSIPYLNIPQEENPFLGYRAVRIYPEFAGLFRTQ 482 Query: 651 LRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAELD------APAVPLG 704 LRA+ RAA G A+ +M PM+ +L ++ ++ ++ EL A + LG Sbjct: 483 LRAILRAASFGNAQ------LMIPMVHSLDQILWVKGEIQKAIVELKRDGLRHAETITLG 536 Query: 705 IMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRL 764 IMVEVP+ D VDFFSIG+ND+TQY A+DR +P ++ + + P+ LR+++ Sbjct: 537 IMVEVPSVCYIIDHFCDEVDFFSIGSNDMTQYLYAVDRNNPRVSPLYNPITPSFLRMLQQ 596 Query: 765 TVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKD 824 V A + G+WVG+CG + G+ LL GLG+ ELSM+ IPAVK +LR D A ++ Sbjct: 597 IVTTAHQRGKWVGICGELGGESRYLPLLLGLGLDELSMSSPRIPAVKSQLRQLDSEACRE 656 Query: 825 AAQRALDCETADAVRAL 841 A++A +C +A + AL Sbjct: 657 LARQACECRSAQEIEAL 673 Score = 38.9 bits (89), Expect = 1e-06 Identities = 38/154 (24%), Positives = 68/154 (44%), Gaps = 13/154 (8%) Query: 7 TAIMPTDLLRP----ELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAAS--MLRREAV 60 TA P + +RP E + + + KE+AI+ L G + + + +RE + Sbjct: 675 TAFTPEEDVRPLLALENIFVDQDFSNKEQAIQFLCGNLGVNGRTEHPFELEEDVWQREEI 734 Query: 61 ANTFLGHGVAIPHGMVEDRGMVRRSGIAVLQVPGGIAWNPGQ-TAHLVVAI---AAQSDA 116 T +G GVAIPH + +R S I++ ++ I W LV+ + A + Sbjct: 735 VTTGVGFGVAIPHTKSQ---WIRHSSISIARLAKPIGWQSEMGEVELVIMLTLGANEGMN 791 Query: 117 HIAVLRRLTRLMQDEARLTALFTVTDPAALAAAL 150 H+ V +L R + ++ +LF D ++ L Sbjct: 792 HVKVFSQLARKLVNKNFRQSLFAAQDAQSILTLL 825 Lambda K H 0.319 0.134 0.387 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: 1196 Number of extensions: 33 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: 2 Length of query: 846 Length of database: 831 Length adjustment: 42 Effective length of query: 804 Effective length of database: 789 Effective search space: 634356 Effective search space used: 634356 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 (21.7 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