Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PfGW456L13_3148 L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3148 Length = 283 Score = 76.3 bits (186), Expect = 6e-19 Identities = 58/195 (29%), Positives = 95/195 (48%), Gaps = 21/195 (10%) Query: 17 IWLASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSLVVNILRSLPF 76 +W+AS+ T ++ ++L +V + PLGVL K V ++NI++++P Sbjct: 87 LWVASMQTIALVSVAVLISVSIAFPLGVLAARV--------KRVDEAFLPILNIMQTVPP 138 Query: 77 IILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEATQAMGA 136 + LI + L SLG AI +V P RL A +++ K +E QA+GA Sbjct: 139 WVYLIPAVMLF------SLGRVPAIIATIVYGIPPMLRLTTLAFKQLPKEFLELGQAIGA 192 Query: 137 STRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIRFGYQRFQ--- 193 S R I++ LP A P ++ + + ++ +AG+VGAGGLG R G R + Sbjct: 193 SPRAILFKIELPTAAPTLLVGLNQCILLSLAMVVLAGLVGAGGLGAEVTR-GLTRMEMGL 251 Query: 194 ---TDVMVVTVVMLL 205 + +V V +LL Sbjct: 252 GLRAGLAIVAVALLL 266 Lambda K H 0.329 0.143 0.419 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: 87 Number of extensions: 6 Number of successful extensions: 1 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: 225 Length of database: 283 Length adjustment: 24 Effective length of query: 201 Effective length of database: 259 Effective search space: 52059 Effective search space used: 52059 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: 46 (22.3 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