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 CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 124 bits (311), Expect = 4e-33 Identities = 79/238 (33%), Positives = 133/238 (55%), Gaps = 13/238 (5%) Query: 11 KPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD 70 KP++ ++ K F GK L AVD +S+ + EGE L+G SGCGK+TL R + P Sbjct: 12 KPIITFENVTKRF--GK--LAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPT 67 Query: 71 GGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKK 130 G+I +G+DI+N+ P ++ + ++FQ ++ P MTV + L + + K Sbjct: 68 EGRILIDGQDISNV-----PPNKRPVNMVFQSY--AVFPHMTVADNVAYGLKVDNV-PKA 119 Query: 131 ERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVS 190 ER RV E L++V +G P + SGGQ+QR+ +ARAL P+ ++ DEP+SALD Sbjct: 120 EREARVAEALELVQLGG-LGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAK 178 Query: 191 IQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNP 248 ++ Q+ L +Q+K+GI+++ + H+ ++ + AVM G + + ++ P Sbjct: 179 LREQMRTELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFP 236 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: 301 Number of extensions: 12 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: 381 Length adjustment: 29 Effective length of query: 299 Effective length of database: 352 Effective search space: 105248 Effective search space used: 105248 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