Align Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale)
to candidate WP_011840356.1 RSPH17029_RS02215 PTS fructose transporter subunit EIIBC
Query= uniprot:G8B0J2 (580 letters) >NCBI__GCF_000015985.1:WP_011840356.1 Length = 581 Score = 676 bits (1745), Expect = 0.0 Identities = 369/581 (63%), Positives = 432/581 (74%), Gaps = 17/581 (2%) Query: 1 MANMLAVIAAGDLSTQAVLAAEALRKAAAALGHTIQVEVRSSLGVRNTLPTGAAQGAQGV 60 M ++AVI+ G A LA EALRKAA LG I VE+R+ V + LP A GA V Sbjct: 1 MTGIVAVISTGSFGPHAALAREALRKAAQGLGRAIAVELRTQETVTDALPPEAVSGASQV 60 Query: 61 ILV---GSGDLGEERFAGLKRSAAALDAVLRDARAVLEQA---LATAPAQAPAQT-GTKK 113 +LV G E RFAG A L VL DA VL + A APA PA G K Sbjct: 61 LLVTEPGGAAADEARFAGRPTIHATLAEVLEDAPGVLARTGSGAAAAPAADPAAAEGALK 120 Query: 114 IVAITSCPTGIAHTFMAAEGIQQAAQALGHAVRVETQGSVGARDTLTEQEIREADVVLIA 173 IVAITSCPTGIAHTFMAAEG+ + A+A GH +RVETQGSVGA+D LT EI AD+V+IA Sbjct: 121 IVAITSCPTGIAHTFMAAEGLVEGARAQGHQIRVETQGSVGAQDELTAAEIAAADLVIIA 180 Query: 174 ADTQVDLARFAGKRVFKSGTKPAINDGRALVERALAEAQPHGTAPALADGVAAGKAAKAE 233 AD QVDL RF GKR+F S TKPAI DG L+ +A AEA+ + G A+ +AA+ E Sbjct: 181 ADKQVDLGRFGGKRLFLSPTKPAITDGAGLIRKAQAEAR-------MQAGSASSEAAQPE 233 Query: 234 HAAAQRSGPYKHLMTGVSFMLPFVVTGGLLIAIAFALGGIYVFEDSQQGTLGNALFQIGA 293 A++ G YKHLMTGVSFMLPFVV GGLLIAIAFALGGIYV+ED GTLG+ LFQIGA Sbjct: 234 ---AKKVGVYKHLMTGVSFMLPFVVAGGLLIAIAFALGGIYVYEDQYAGTLGHTLFQIGA 290 Query: 294 KGAFALMVPALAGYIAFSIADRPGITPGMVGGILAANLGAGFLGGIVAGFIAGYATSFLN 353 KGAF LMVPALAGYIA+SIADRPG+ PGM GG++A +GAGFLGGIVAGFIAGY +LN Sbjct: 291 KGAFTLMVPALAGYIAWSIADRPGLAPGMTGGVIAGTIGAGFLGGIVAGFIAGYGVLWLN 350 Query: 354 RNIRLHKNLEGLKPVLILPLLGSLVTGLAMIYVVGAPVAEALATLSAWLKGMQGSSAILL 413 R I+L K L+GLKPVLILPLLG+ +TGL M YVVG P A LAT++A+L+GMQG+SA LL Sbjct: 351 RAIKLPKTLQGLKPVLILPLLGTALTGLLMYYVVGEPTARLLATITAFLQGMQGTSAALL 410 Query: 414 GLLIGAMMAFDMGGPVNKAAYAFSTGLIASQVYTPMAAAMAAGMVPPLGLALATKLFADR 473 GLL+G MMA DMGGPVNKAAYAF+T LIA+ V PMAA M AGMVPP+ LA+A +L R Sbjct: 411 GLLLGGMMAVDMGGPVNKAAYAFATTLIAANVLEPMAAVMCAGMVPPIALAVACRLLPAR 470 Query: 474 FTREEREAGNAAGILGIAFITEGAIPFAARDPLRVIPALVLGAALTGAISMGIGAELKVP 533 FT EEREAGNAA +LG+AF+TEGAIPFAARDPLRVIP+L+ G+A+ GAI M +G +VP Sbjct: 471 FTPEEREAGNAAFVLGLAFVTEGAIPFAARDPLRVIPSLIAGSAVAGAICMALGVAQRVP 530 Query: 534 HGGIFVLPIPNAVTHLAGYVVALVAGTVTTAVALRFLKRPV 574 HGGIFVLPIPNAVT+L G+ +ALVAGTV + VAL +KR + Sbjct: 531 HGGIFVLPIPNAVTNLTGFGIALVAGTVVSVVALALVKRRI 571 Lambda K H 0.321 0.135 0.378 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: 981 Number of extensions: 41 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: 580 Length of database: 581 Length adjustment: 36 Effective length of query: 544 Effective length of database: 545 Effective search space: 296480 Effective search space used: 296480 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. 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