Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337 Length = 575 Score = 797 bits (2058), Expect = 0.0 Identities = 417/570 (73%), Positives = 473/570 (82%), Gaps = 2/570 (0%) Query: 6 VTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVLLVGVE 65 VTACP G VTSVL ARLL AA+R GW T VE + + PE +LSA + A+WVLLV Sbjct: 1 VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60 Query: 66 PLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLV-APEAGAAPRIVA 124 P+ +RFVGK ++R+ PA AL D + L+R A A V +A D A APR+VA Sbjct: 61 PVDMSRFVGKRLFRSTPALALQDVDSVLRRGAEEAEVFLASDVVEQAPAVSTDRAPRLVA 120 Query: 125 VTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLLAADI 184 +TACPTGVAHTFMAAEALQ AA +LG+ LQVETQGSVGARNPL IA ADVVLLA DI Sbjct: 121 ITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLLATDI 180 Query: 185 DVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVYKHLL 244 +V T RFAGKKIYRC TG+ALKQA ATL +AL EG+ ESA + ++ A+ EK GVYKHLL Sbjct: 181 EVATERFAGKKIYRCSTGIALKQAEATLNKALVEGRQESASSGASAPAKSEKTGVYKHLL 240 Query: 245 TGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPMLAGYIAY 303 TGVSFMLPMVVAGGL+IALS FGI+A+K+PG+LAA L +G DTAF LMVP+LAGYIAY Sbjct: 241 TGVSFMLPMVVAGGLMIALSFVFGIEAFKEPGTLAAALMQIGGDTAFKLMVPLLAGYIAY 300 Query: 304 SIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKPILV 363 SIADRPGLAPGM+GG+LA TLGAGFIGGI+AGF+AGYAA+AIS RLP SLEALKPIL+ Sbjct: 301 SIADRPGLAPGMIGGMLASTLGAGFIGGIIAGFLAGYAAKAISRYARLPQSLEALKPILI 360 Query: 364 IPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGGPVN 423 IPLLASL TGL+M+Y+VGKPVAGML ALT FLD MGT+NAILLG+LLG MMCVDLGGP+N Sbjct: 361 IPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAILLGVLLGAMMCVDLGGPIN 420 Query: 424 KAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASVLGL 483 KAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT +ARRKFA++ER+AGKAA VLGL Sbjct: 421 KAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGL 480 Query: 484 CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAINHAL 543 CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFVML+PNAINHAL Sbjct: 481 CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHAL 540 Query: 544 AYLLAIVAGSLLTGLLYAVLKRGAEPGLAL 573 YLLAIVAGSLLTG+ YA+LKR +AL Sbjct: 541 LYLLAIVAGSLLTGVAYALLKRPEVVEMAL 570 Lambda K H 0.321 0.137 0.392 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: 933 Number of extensions: 40 Number of successful extensions: 7 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: 585 Length of database: 575 Length adjustment: 36 Effective length of query: 549 Effective length of database: 539 Effective search space: 295911 Effective search space used: 295911 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 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