Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 143 bits (361), Expect = 5e-39 Identities = 107/283 (37%), Positives = 146/283 (51%), Gaps = 11/283 (3%) Query: 59 ILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVA-GFSLPIVLLSALGT 117 IL + VA++AIG TLVI T GIDLS G VMA+ G M G S P+ + + Sbjct: 43 ILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMALGGIVMTKMAADYGLSAPVAIACGMAV 102 Query: 118 GILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLF 177 +L GL NG+LV +K+ PF+ TL + QL + Q +T ++ G+ L Sbjct: 103 TMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAATQLYSGAQTITDIPAGMTALGNTFQLG 162 Query: 178 LPTPVIIAVLTLILF---WLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSG 234 V AVL L L+ W R+TA G + AVG + A + G+ T +++ YVL+G Sbjct: 163 QTAIVWGAVLMLALYLVTWFALRETAPGRHVYAVGNSPEATRLTGIATDKVLLGVYVLAG 222 Query: 235 LCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQG 294 L IA ++ A GA NAG LDAI AVV+GG SL GGR +L ++VGALI+ Sbjct: 223 LFYGIASLLSVART-GAGDPNAGQTENLDAISAVVLGGTSLFGGRGVILGTLVGALIVGV 281 Query: 295 MNTGILLSGFPPEMNQVVKAV-VVLCVLIVQSQRFISLIKGVR 336 G+ L G +V + V+L V Q R KGVR Sbjct: 282 FRNGLTLMGVSSVYQILVTGILVILAVATDQLSR-----KGVR 319 Lambda K H 0.327 0.142 0.416 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: 273 Number of extensions: 20 Number of successful extensions: 4 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: 341 Length of database: 319 Length adjustment: 28 Effective length of query: 313 Effective length of database: 291 Effective search space: 91083 Effective search space used: 91083 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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