Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Dsui_2800 Dsui_2800 ABC-type dipeptide/oligopeptide/nickel transport system, permease component
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__PS:Dsui_2800 Length = 482 Score = 129 bits (324), Expect = 1e-34 Identities = 87/295 (29%), Positives = 142/295 (48%), Gaps = 35/295 (11%) Query: 13 WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTD 72 W+ W R + + + + +L P +A P E H + GTD Sbjct: 201 WRDLWWRPPTSTAPAWDALLLTLAGLFLLLTPLLALAP--EYH------------VLGTD 246 Query: 73 ALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAF 132 +G+D+ +L S+R + +IG + V L IG +LG AG+ GW+D I + + + Sbjct: 247 KVGQDILYLVLKSIRTSLVIGLVTTLVTLPIGVLLGISAGYFRGWVDDLIQYLYSTLNSI 306 Query: 133 PTFLFNVILV---------------TALGRG---LFTIFLAIGLTGWAGMARLVRGQVLY 174 P+ L V TA R L + +G+T W G+ARL+RG+ L Sbjct: 307 PSVLLIAAAVLMMQVVIDTHPEWFATAAERADLRLLALCFILGMTSWTGLARLLRGEALK 366 Query: 175 LKNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRP 234 L E+++AA++ G S++ I+ +HILPN++ +L+ L +MTE+ L+ + +GV P Sbjct: 367 LSQLEYIQAAQSFGVSSWRILLRHILPNVMHIVLIALVMDFSSLVMTEAVLSYLEIGVDP 426 Query: 235 PMPSWGNLIGEGIGMMMAFPHLLIFPAVTFAFTLI---SFTFLADGLRDAFNPRS 286 M S+G+LI + P + A F F I + AD +RDAF+PR+ Sbjct: 427 TMVSFGSLINNARMELAREPMVWWSLAAAFVFMFILVLAANLFADVVRDAFDPRA 481 Lambda K H 0.331 0.147 0.457 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: 13 Number of successful extensions: 3 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: 289 Length of database: 482 Length adjustment: 30 Effective length of query: 259 Effective length of database: 452 Effective search space: 117068 Effective search space used: 117068 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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