Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 7026015 Shewana3_3163 sodium:dicarboxylate symporter (RefSeq)
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__ANA3:7026015 Length = 417 Score = 233 bits (595), Expect = 7e-66 Identities = 134/414 (32%), Positives = 225/414 (54%), Gaps = 22/414 (5%) Query: 3 TRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSG 62 +R P ++ + I+ +G+LLG +T LKPLGD FI IKM++AP++FC +V Sbjct: 7 SRIPFWQKVLAGFILGALVGVLLG----ETATVLKPLGDLFISAIKMLVAPLVFCAIVVS 62 Query: 63 IAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAY 122 I + + ++ + L F + T+A LIGL V +++ G M + + + Sbjct: 63 ITSLGSQTNLKRLSLKTLGMFMLTGTVASLIGLAVGSLIDMGGTMQLATTEV-------- 114 Query: 123 VTAGKDQSIVGF---ILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179 ++++I GF +L++IP + A+G +LQ+++F+ + G A++++G +P+ Sbjct: 115 ----RERNIPGFAQVLLDMIPVNPFASLADGKVLQIIVFAALVGIAINKVGEKAEPLKRT 170 Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239 I+ A VMF + M++KL PIG G MA+ +G YG+ +L+ LG+ + YI ++ ++ V Sbjct: 171 IEAGAEVMFQLTRMVLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIAAIYIAALIHMIFV 230 Query: 240 LGAICR-AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPT 298 G + + A G S ++ R L+ TSSS LP +E +G K V+P Sbjct: 231 YGGLVKFAAGLSPVQFFRKAMPAQLVAFSTSSSFGTLPASTRAVETMGVSKRYSAFVMPL 290 Query: 299 GYSFNLDGT-SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLA 357 G + N+DG IY +AA+FIAQ +D + + + ++S G AGV GS ++L Sbjct: 291 GATMNMDGCGGIYPAIAAIFIAQIYGIPLDTLDYVMIAVTATVASVGTAGVPGSAMVMLT 350 Query: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQ 411 TL +G LP+ G+A I IDR + R TN+ G+ + VV+ K ELD +Q Sbjct: 351 VTLGVIG-LPLEGIAFIAAIDRIIDMIRTATNVTGDMMTAVVIGKSENELDVEQ 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: 441 Number of extensions: 30 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