Align D-serine transporter DsdX (characterized)
to candidate Echvi_2089 Echvi_2089 gluconate transporter
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__Cola:Echvi_2089 Length = 438 Score = 261 bits (668), Expect = 2e-74 Identities = 141/436 (32%), Positives = 248/436 (56%), Gaps = 5/436 (1%) Query: 11 LLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVI 70 +L+SI+L+VL IV K +PF+A L+ S G ++G+ P + +++ G+G LG L +I Sbjct: 6 VLLSILLLVLLIVWAKLNPFIAFLITSIVAGLLLGIPPEQVAVSVQQGMGSLLGDLVIII 65 Query: 71 GLGTILGKMMEVSGAAERIGLTLQRCRWLS-VDVIMVLVGLICGITLFVEVGVVLLIPLA 129 +G +LGK++ SGAA+RI L R + M++ GL+ GI LF VG VLL+PL Sbjct: 66 TMGAMLGKLVAESGAAQRIADFLMRVFGKKYIHWAMMVTGLVVGIPLFYNVGFVLLVPLV 125 Query: 130 FSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMA 189 F++A + S + + IPL AL H +PPHP+ + + A++G ++YG++V + Sbjct: 126 FTVAHQYKLSAVYVGIPLLAALSVTHGFLPPHPSPAALVAQFDANMGVTLLYGMMVAIPT 185 Query: 190 SLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTILLPIALMLVKTIAE 249 L+ GP F +FL + +P P+ + A K +E LP + + LLP+ L++ + Sbjct: 186 ILVAGPFFARFL-KHIPASPLKSFRASSKPEEE--LPGTINSFLSALLPVVLLVGTPVLL 242 Query: 250 LNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSIANIL 309 + +S LY V+FI +P M ++ VA + LG+ Q M M ++ + +A I+ Sbjct: 243 MQTDEQSALYGYVKFIADPGMVMLFSLLVATFTLGLHQGMKMDHLMDIYVDSVKDVAMII 302 Query: 310 LIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMMGATA 369 LI+ GA +L S ++ +A L ++HP++LAW + ++ VGSATVA + Sbjct: 303 LIVAGAGALKQVLLDSGVSQVIADGLEGWNVHPLVLAWTITAVIRVCVGSATVAGLTTAG 362 Query: 370 IVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYYTTATFI 429 I+AP++ + P ++ +AIG+G++ + D+ FW+ K++ ++ +T + ++ I Sbjct: 363 IIAPLIE-GSGVDPNLVVLAIGAGSLMFSHFNDAGFWMYKEFFNVSIKDTIRSWSVMETI 421 Query: 430 ASVVALAGTFLLSFII 445 +VV LAG +L +++ Sbjct: 422 VAVVGLAGVMVLDWVV 437 Lambda K H 0.329 0.143 0.418 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: 502 Number of extensions: 33 Number of successful extensions: 6 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: 445 Length of database: 438 Length adjustment: 32 Effective length of query: 413 Effective length of database: 406 Effective search space: 167678 Effective search space used: 167678 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: 51 (24.3 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