Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 6936881 Sama_1055 sodium:dicarboxylate symporter (RefSeq)
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__SB2B:6936881 Length = 417 Score = 226 bits (576), Expect = 1e-63 Identities = 137/410 (33%), Positives = 218/410 (53%), Gaps = 13/410 (3%) Query: 5 QPLYKSLYFQVIVA-IAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 Q L K ++Q ++A A+GIL G ++ LKPLGD FI IKM++AP++ C +V I Sbjct: 4 QTLNKIPFWQKVLAGFALGILTGVLLGESATVLKPLGDLFIAAIKMLVAPLVLCAIVVSI 63 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 + + ++ + L F + T+A LIGL V + G M L +++V V Sbjct: 64 TSLGSSSNLKRLSFKTLALFMLTGTLASLIGLAVGSSFDMGGSMQ-----LASTEVRERV 118 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 G Q +L++IP + NG +LQ+++F+ + G A++ +G +P+ D Sbjct: 119 VPGFAQ----VLLDMIPVNPFASLTNGKVLQIIVFAALVGIAINAVGEKAEPLKKVFDAG 174 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 A VMF + M++KL PIG G MA+ +G YG+ +L+ LG+ +I Y+ ++ ++ V G + Sbjct: 175 AEVMFQLTRMVLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIIAIYVAALIHIVFVYGGL 234 Query: 244 CR-AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSF 302 + A S L+ R L+ T+SS LP E +G K V+P G + Sbjct: 235 VKFAARLSPLQFFRKAMPAQLVAFSTASSFGTLPVTTKCAESMGVSKRYSAFVLPMGATM 294 Query: 303 NLDGT-SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLS 361 N+DG IY +AA+FIAQ +D+T + + + ++S G AGV GS ++L TL Sbjct: 295 NMDGCGGIYPAIAAIFIAQIYGIPLDMTDYMLIAVTATVASVGTAGVPGSAMVMLTVTLG 354 Query: 362 AVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQ 411 VG LP+ G+A I IDR + R TN+ G+ + VVV ELD ++ Sbjct: 355 VVG-LPLEGIAFIAAIDRVIDMIRTCTNVTGDMMTAVVVGNSEGELDRER 403 Lambda K H 0.326 0.142 0.402 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: 446 Number of extensions: 31 Number of successful extensions: 5 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: 444 Length of database: 417 Length adjustment: 32 Effective length of query: 412 Effective length of database: 385 Effective search space: 158620 Effective search space used: 158620 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 (21.6 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