Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 771 bits (1992), Expect = 0.0 Identities = 410/575 (71%), Positives = 471/575 (81%), Gaps = 6/575 (1%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 M L IVTACP G VTSVL +RLL AA RLGW T VE + L+ QIA AD V+ Sbjct: 1 MNLLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVV 60 Query: 61 LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120 +V PL+ RFVGK V ++ P+EAL DP AFL+ AA AS DEA A P Sbjct: 61 VVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAE--AAHTSGKP 118 Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180 ++VAVTACPTGVAHTFMAAEALQ AA + G+ LQVET+GSVGARN L+ IAAADVVLL Sbjct: 119 KLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLL 178 Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVA---RDEKR 237 AADI+VD ARFAGK+++RCGTGVALKQ ATL+RAL EG V S A + + + EK Sbjct: 179 AADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVLSGNAVATSASGEKKGEKT 238 Query: 238 GVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPM 296 GVYKH+LTGVS+MLPMVVAGGLLIALS FGI+A+K+ G+LAA L +G +TAF LMVP+ Sbjct: 239 GVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKEEGTLAAALMKIGGETAFQLMVPL 298 Query: 297 LAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLE 356 LAGYIAYSIADRPGLAPGM+GGLLAGTLGAGFIGGI+AGF+AGYAA+A+S + LPAS+E Sbjct: 299 LAGYIAYSIADRPGLAPGMIGGLLAGTLGAGFIGGIIAGFVAGYAAKAVSRWIPLPASIE 358 Query: 357 ALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCV 416 +LKPIL+IPLLASLVTGL+M+Y+VG PVA +LA LT FLD MGTSNAILLGLLLG MMCV Sbjct: 359 SLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTMGTSNAILLGLLLGTMMCV 418 Query: 417 DLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGK 476 DLGGPVNKAAYAFSVGLL+S SYAPMAA MAAGMVPPIGMG+ATL+ARRKFA++ER+AGK Sbjct: 419 DLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGIATLIARRKFAQTEREAGK 478 Query: 477 AASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVP 536 AA VLG CFISEGAIPFAAKDPLRVIPASIAGGALTGALSM FG KL APHGGLFV+L+P Sbjct: 479 AALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMAFGAKLLAPHGGLFVLLIP 538 Query: 537 NAINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGL 571 NAINHAL YL+AI+AGSL+TG++YAV+K+ GL Sbjct: 539 NAINHALLYLVAILAGSLVTGVIYAVIKQSEPQGL 573 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: 940 Number of extensions: 44 Number of successful extensions: 9 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: 585 Length of database: 579 Length adjustment: 36 Effective length of query: 549 Effective length of database: 543 Effective search space: 298107 Effective search space used: 298107 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