Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 809 bits (2089), Expect = 0.0 Identities = 427/581 (73%), Positives = 483/581 (83%), Gaps = 5/581 (0%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 M +AIVTACP GQV+SVL+ARLL AA+R GW T VE PE +LSA QIAEADWVL Sbjct: 1 MNIAIVTACPNGQVSSVLSARLLSAAAQRRGWSTSVEVQNTEHPERQLSAAQIAEADWVL 60 Query: 61 LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120 +V P+ ARFVGK +Y++ P++ALAD FL AAA A + A A A AGA Sbjct: 61 VVSTGPVDLARFVGKRLYQSTPSQALADREGFLDEAAANAELLAAVTGAPAAASSAGA-- 118 Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180 RIVAVTACPTGVAHTFMAAEALQ AA QLG+ L VETQGSVGARNPL IAAADVVLL Sbjct: 119 RIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQGSVGARNPLSAEAIAAADVVLL 178 Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVA--RDEKRG 238 AADI+V TARFAGK+IYRCGTG+ALKQARATL++ALA+ VE+ A+A + EK G Sbjct: 179 AADIEVPTARFAGKRIYRCGTGIALKQARATLDKALAQATVENGADAAAATTPTKSEKTG 238 Query: 239 VYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPML 297 VYKHLLTGVSFMLPMVVAGGLLIALS FGI+AYK+ G+L A L +G + AF LMVP+L Sbjct: 239 VYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAYKEAGTLPAALMQIGGEAAFKLMVPLL 298 Query: 298 AGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEA 357 AGYIA+SIADRPGLAPGM+GGLLA TLGAGFIGGIVAGF+AGY+A+AI+ RLP+SLEA Sbjct: 299 AGYIAWSIADRPGLAPGMIGGLLASTLGAGFIGGIVAGFLAGYSAKAIARWARLPSSLEA 358 Query: 358 LKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVD 417 LKPIL+IPLLASL TGL+M+YVVG+PVA ML LT FLD MGT+NAILLGLLLGGMMCVD Sbjct: 359 LKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHFLDSMGTTNAILLGLLLGGMMCVD 418 Query: 418 LGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKA 477 LGGP+NKAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT LARRKFA+SER+AGKA Sbjct: 419 LGGPINKAAYAFSVGLLASSSYAPMAATMAAGMVPPIGLGIATFLARRKFAQSEREAGKA 478 Query: 478 ASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPN 537 A LGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFV+L+PN Sbjct: 479 ALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVLLIPN 538 Query: 538 AINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLALGTSSS 578 AINHAL YLLAIVAGSL+T ++YAV+K+ LA+ + S Sbjct: 539 AINHALLYLLAIVAGSLVTAVVYAVIKKSERVELAVAPAKS 579 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: 926 Number of extensions: 39 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: 585 Length of database: 580 Length adjustment: 36 Effective length of query: 549 Effective length of database: 544 Effective search space: 298656 Effective search space used: 298656 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