Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 115 bits (289), Expect = 1e-30 Identities = 78/236 (33%), Positives = 126/236 (53%), Gaps = 11/236 (4%) Query: 15 QTVDLKKYFPQGKRI--LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGG 72 Q V L ++ KR AV+ + + I +GE L+G SGCGK+TL R + P G Sbjct: 18 QAVPLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTG 77 Query: 73 KIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKER 132 +I +G+D+T E+ PY + + ++FQ +L P M+V I L + K Sbjct: 78 RILIDGQDVT-----EVPPYERPVNMMFQSY--ALFPHMSVADNIAFGLKQDGLA-KPVI 129 Query: 133 RKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQ 192 + +V L++V +GR F PH+ SGGQ+QR+ +AR LA PK ++ DEP++ALD ++ Sbjct: 130 KDKVAAALELVQMGR-FSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLR 188 Query: 193 AQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNP 248 L IQ ++GI+++ + H+ +S ++ VM G I + G I+ P Sbjct: 189 EATQLELVNIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYP 244 Lambda K H 0.321 0.142 0.417 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: 319 Number of extensions: 22 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: 328 Length of database: 379 Length adjustment: 29 Effective length of query: 299 Effective length of database: 350 Effective search space: 104650 Effective search space used: 104650 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 (21.8 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