Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >NCBI__GCF_003217235.1:WP_110753066.1 Length = 274 Score = 167 bits (423), Expect = 2e-46 Identities = 96/272 (35%), Positives = 153/272 (56%), Gaps = 13/272 (4%) Query: 21 GLFLAMLVICLPGL----WIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGV 76 G L + VI P + W++ SL+ ++ A PP+ IPE + Y +F+ Sbjct: 11 GTALLVFVIVSPAIFFFVWMLSLSLKYEIDNGAYPPILIPERFAWSNYTQIFAEND---- 66 Query: 77 PVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLP 136 YF NSL+V+ +T++AL +G+ GY AR + KSA+ + M+ R PG++ +P Sbjct: 67 -FLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAH-KSAVVI--MIARMTPGLSYLIP 122 Query: 137 LFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFW 196 LF+L+ G++ T + I+ ++ + VP IW++ G+F P +L EAAQIDG WQ F Sbjct: 123 LFLLFQTLGLLGTLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEAAQIDGANAWQVFR 182 Query: 197 QVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMC 256 V P+A PGI + I A + SWN + + S ++TLPV + + + + W + Sbjct: 183 LVALPIAKPGIVVSLILAVIFSWNNFVFGI-VLASRETRTLPVAVYNMLSFEQVSWGPLA 241 Query: 257 ALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG 288 A A+V+ +P L LT + Q+ +V+GLT GAVKG Sbjct: 242 AAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273 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: 249 Number of extensions: 19 Number of successful extensions: 4 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: 274 Length adjustment: 26 Effective length of query: 262 Effective length of database: 248 Effective search space: 64976 Effective search space used: 64976 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 24 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