Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate 203494 SO4417 anaerobic C4-dicarboxylate membrane transporter (NCBI ptt file)
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__MR1:203494 Length = 447 Score = 357 bits (915), Expect = e-103 Identities = 180/447 (40%), Positives = 280/447 (62%), Gaps = 9/447 (2%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 M E +L L++G R GG+ LG++ G+G+ ++ F+FGL P PP+ V+L IL+V+ Sbjct: 1 MILMEFIVVLGCLLLGTRYGGMGLGLISGIGLFLLTFVFGLAPGQPPVQVMLTILAVIGC 60 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 AA LQ +GGLD++++ AE++LRRHP+YIT+LAP + TF+ GTGHVVY++ P+IS++A Sbjct: 61 AAVLQTAGGLDVMMQFAERLLRRHPQYITILAPLTTWTLTFLCGTGHVVYTMFPIISDIA 120 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPL-----GVSISTIMMICVPA 175 IRPERP++++ +ASQ AI ASP+S A+ +M+ ++A S+ I+M+ VPA Sbjct: 121 LKKNIRPERPMAVASVASQMAICASPVSVAVVSMVSILAAQQGVGHAYSMLEILMVSVPA 180 Query: 176 TLIGVAMGAIATFNKGKELKDDPEYQRRLAE----GLIKPAQKESKNTVVTSRAKLSVAL 231 +L GV + A+ + +GK+L D E+Q R+ + I + N +A + + Sbjct: 181 SLCGVLVAALWSLRRGKDLDKDEEFQERIQDPVQRAFIYDKGETLLNQTFPKQAYWATGI 240 Query: 232 FLTSAIVIVLLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIIS 291 F + +VLLG LRP+ E L PLSM+ IQ+ ML I++ C+ + +I + Sbjct: 241 FFAAIAAVVLLGSFSELRPVFEEKGKLAPLSMNLVIQMMMLIAGAFILMSCKVKPAEIAN 300 Query: 292 GTVFRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSS 351 G VF+AG +AI FG+AWMS+TF H+ ++K + ++Q W A+++F +S +V+S Sbjct: 301 GPVFKAGMVAIFSVFGVAWMSDTFFISHMDVLKENLSHVVQNQPWTYALVLFLISKLVNS 360 Query: 352 QAATTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVL 411 QAA + P+GLALG+ LI PA GYF +P LA + FD +GTT+IGK+++ Sbjct: 361 QAAALTAIAPMGLALGVDPKLLIAFLPASYGYFVLPTYPSDLACIGFDRSGTTKIGKFII 420 Query: 412 NHSFMRPGLVNVIVSVIVGLLIGKMVL 438 NHSF+ PGL+ V + VG L+ +L Sbjct: 421 NHSFIIPGLIGVGTASTVGYLLATALL 447 Lambda K H 0.328 0.141 0.409 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: 415 Number of extensions: 13 Number of successful extensions: 3 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: 439 Length of database: 447 Length adjustment: 32 Effective length of query: 407 Effective length of database: 415 Effective search space: 168905 Effective search space used: 168905 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