Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 (characterized)
to candidate SM_b20327 SM_b20327 trehalosemaltose transporter permease
Query= reanno::WCS417:GFF2491 (276 letters) >FitnessBrowser__Smeli:SM_b20327 Length = 276 Score = 143 bits (361), Expect = 4e-39 Identities = 85/266 (31%), Positives = 141/266 (53%), Gaps = 10/266 (3%) Query: 17 LAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPT---LENYLHINERSNYFSYAW 73 L I ++ FP ++ +LTS K+ F + + PT L NY I + Sbjct: 14 LVAVIILVAVFPFYYAILTSLKSGTALF----RIDYWPTDISLANYAGIFSHGTFVRNLG 69 Query: 74 NSVLISFSATALCLLISVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVGVLMPIYLLAKS 133 NS+L++ A+ LL++V AAY++A + LL +LS M P + VL ++ L + Sbjct: 70 NSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRF 129 Query: 134 FGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIA 193 G+ +T +ALI Y + LP VW++ T+ +D+P +I EAA +DGA+ W + RV +P+ Sbjct: 130 VGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLM 189 Query: 194 KGGLASTVLLSLILCWNEAFWSLNLTSSS---AAPLTALIASYSSPEGLFWAKLSAVSTL 250 L +T LL+ I WNE ++L TSS+ P+ + S S + W + A S + Sbjct: 190 WPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVI 249 Query: 251 ACAPILIFGWISQKQLVRGLSFGAVK 276 P+++ I Q++++ GL+ G VK Sbjct: 250 VTVPLVVLVLIFQRRIISGLTAGGVK 275 Score = 23.5 bits (49), Expect = 0.005 Identities = 19/103 (18%), Positives = 41/103 (39%), Gaps = 18/103 (17%) Query: 15 GTLAWAIAILIFFPIFWMVLTSFKTEIDAF-ATPPQFIFTPTLEN---------YLHINE 64 G W + +F P+ W L + T + AF A +F+F T + + + Sbjct: 174 GASPWVVITRVFMPLMWPALVT--TGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLS 231 Query: 65 RSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETQRTKG 107 + F W +++ A ++++VP + ++ + G Sbjct: 232 GGSQFEIPWGNIM------AASVIVTVPLVVLVLIFQRRIISG 268 Lambda K H 0.327 0.138 0.427 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: 222 Number of extensions: 15 Number of successful extensions: 5 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 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: 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