Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate 7025533 Shewana3_2684 gluconate transporter (RefSeq)
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__ANA3:7025533 Length = 452 Score = 216 bits (550), Expect = 1e-60 Identities = 150/453 (33%), Positives = 240/453 (52%), Gaps = 18/453 (3%) Query: 7 VVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFL 66 +V L+ I IV+ KFK HPFL L+LA+F G+ D+ I +G G LG++ Sbjct: 3 LVLILIGVIAFIVIATSKFKLHPFLTLILAAFIAAFAYGLPSGDIAKTITTGFGNILGYI 62 Query: 67 AAVIGLGTILGKMMEVSGAAERIG-LTLQRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125 VI LGTI+G ++E SGAA + + ++ + M ++G + I +F + G V+L Sbjct: 63 GLVIVLGTIIGIILEKSGAAITMADVVIKVLGKRFPTLTMSIIGYLVSIPVFCDSGFVIL 122 Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLG--ADIGSVIVYGL 183 L S+A + S + +++ L T L A H VPP P + A LG +++G VI GL Sbjct: 123 NSLKQSMANRMKVSSVSMSVALATGLYATHTFVPPTPGPIAAAGNLGLESNLGLVIGVGL 182 Query: 184 LVGLMASLIGGPLFLKFLGQR------LPFKPVPTEFADLKVRDEKTLPSLGATLFTVLL 237 LV +A+L G +F K +F LK + TLPS + + Sbjct: 183 LVAAVAALAGMFWANRFASVEPDGEGAEELKAQAADFEALK-QSYGTLPSPLKAFAPIFV 241 Query: 238 PIALMLVKTIAELNMA--RESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTML 295 PI L+ + +IA A + GL++LL F+G P+ A I +F++ +L ++ + Sbjct: 242 PILLICLGSIANFPSAPLGKEGLFSLLVFLGQPVNALLIGLFLS--LLLLKSDNKIAEFS 299 Query: 296 THTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHA 355 G + A I+LI GAGGAF A+LK++ + D L LS + + I + ++VA L + Sbjct: 300 ERISQGLVAAAPIILITGAGGAFGAVLKATPIGDFLGSSLSALGV-GIFMPFIVAAALKS 358 Query: 356 AVGSATVAMMGATAIVAPML---PLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYC 412 A GS+TVA++ +A+VAPML L D+ + +AIG+GA+ + DS FW+V Q+ Sbjct: 359 AQGSSTVALVATSALVAPMLGDIGLGSDMGRVLTVMAIGAGAMTVSHANDSFFWVVTQFS 418 Query: 413 GATLNETFKYYTTATFIASVIALAGTFLLSFII 445 ++ + +K T AT I V A+ ++LS ++ Sbjct: 419 RMSVKQAYKAQTMATLIQGVTAMLTVYVLSLVL 451 Lambda K H 0.328 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: 513 Number of extensions: 32 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: 452 Length adjustment: 33 Effective length of query: 412 Effective length of database: 419 Effective search space: 172628 Effective search space used: 172628 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