Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate HSERO_RS02200 HSERO_RS02200 mannitol ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__HerbieS:HSERO_RS02200 Length = 271 Score = 153 bits (386), Expect = 5e-42 Identities = 81/261 (31%), Positives = 144/261 (55%), Gaps = 9/261 (3%) Query: 27 LVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSL 86 +V+ P W+ +++ + + V++P +L+ +R +FS + G Y +NSL Sbjct: 20 IVLFFPIFWVAVTAFKTESQAYTPSLVFLP---TLETFREVFSRSHYLG-----YVQNSL 71 Query: 87 IVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGI 146 IVS+ ST+++L + + Y+ A + + L + T+ +P + + +P++++ TG+ Sbjct: 72 IVSLGSTLLSLLLAVPAAYSMAFFPTGRTQKLLLWMLSTKMMPAVGVLIPIYLMAKNTGL 131 Query: 147 IDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPG 206 +DT L + Y +N+P +W+ +F VPK++ EAA+IDG WQ + P A PG Sbjct: 132 LDTVTGLTIIYTLINLPIAVWMAFTYFNDVPKEILEAARIDGANAWQEMIYLLLPTAMPG 191 Query: 207 IASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPA 266 +AS + + SWNE + +T SVN+ L V + Y+ + W + A +++ I P Sbjct: 192 LASTALLLVILSWNEAFWSLNLT-SVNAAPLTVFIASYSNPEGLFWAKLSAASLLAIAPI 250 Query: 267 LTLTFIIQKHLVSGLTFGAVK 287 + L ++ QK LV GLTFGAVK Sbjct: 251 MALGWLAQKQLVRGLTFGAVK 271 Lambda K H 0.328 0.141 0.442 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: 240 Number of extensions: 9 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: 288 Length of database: 271 Length adjustment: 26 Effective length of query: 262 Effective length of database: 245 Effective search space: 64190 Effective search space used: 64190 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: 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