Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF1859 Psest_1898 ABC-type sugar transport system, permease component
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__psRCH2:GFF1859 Length = 280 Score = 266 bits (681), Expect = 3e-76 Identities = 131/270 (48%), Positives = 180/270 (66%), Gaps = 2/270 (0%) Query: 1 MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFR 60 +GR +Y LLL +L+P+ +++LT+ K P I + WP + TAW++ Sbjct: 11 LGRLTIYATLLLACAVYLVPLIVMLLTSFKTPEDIRTGNLLSWPEAFSAMGWLTAWDSIG 70 Query: 61 PKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQ 120 F NSV + + A L+S +G+LNGYVL+ W FRGS L F L+LFG F+P+Q IL+P Sbjct: 71 GYFWNSVKIVIPAVLISTALGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQVILLPASF 130 Query: 121 FMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVI 180 + +GL + GLVLVHV+YG+ TL FRN+Y +PD LV AAR+DGAGFF IF ++ Sbjct: 131 TLGKLGLANTTTGLVLVHVVYGLAFTTLFFRNFYVSVPDALVRAARLDGAGFFTIFGRIL 190 Query: 181 LPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAGGE--AVKWNLPMAG 238 LP+SVP +V IWQFTQIWN+FLF V ++QP+TVAL L A ++N+ MA Sbjct: 191 LPMSVPIIMVCLIWQFTQIWNDFLFGVVFASGDTQPVTVALNNLVNTSTGAKQYNVDMAA 250 Query: 239 AILAALPTLLVYILLGRYFLRGLLAGSVKG 268 A++A LPTL+VY++ G+YFLRGL AG+VKG Sbjct: 251 AMIAGLPTLVVYVVAGKYFLRGLTAGAVKG 280 Lambda K H 0.330 0.146 0.461 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: 296 Number of extensions: 13 Number of successful extensions: 2 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: 268 Length of database: 280 Length adjustment: 25 Effective length of query: 243 Effective length of database: 255 Effective search space: 61965 Effective search space used: 61965 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 (21.8 bits) S2: 47 (22.7 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