Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 352708 BT3181 putative sulfate transporter, permease (NCBI ptt file)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Btheta:352708 Length = 559 Score = 355 bits (910), Expect = e-102 Identities = 201/567 (35%), Positives = 323/567 (56%), Gaps = 43/567 (7%) Query: 12 FRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIV 71 F+ + +C K Y+ F DL+AG+ VGI+A+PLA+A I SGV+P+ G+ TA +AG + Sbjct: 6 FKPKLVSCLKN-YSKETFMADLMAGVIVGIVALPLAIAFGIASGVSPEKGIITAIIAGFI 64 Query: 72 IALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131 I+L GGS+ + GPT AF+VI+Y + QQ+G AGL+VATL++G+ LIL+G+ + G +I++I Sbjct: 65 ISLLGGSKVQIGGPTGAFIVIIYGIIQQYGEAGLIVATLMAGVLLILLGVFKLGAVIKFI 124 Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMA--HVPEHYLQKVGALFMALPTINVGDAAIG 189 P + +GFTSGI +TI T QI D GL VP ++ K F T+N + + Sbjct: 125 PYPIIVGFTSGIAVTIFTTQIADIFGLSFGGEKVPGDFVGKWMIYFRHFDTVNWWNTIVS 184 Query: 190 IVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGG--HVATIGSQFHYVLADGSQG 247 IV++ I+ PR ++PG L A++ + ++ GG + TIG +F Sbjct: 185 IVSIIIIAITPRFSKKIPGSLIAIIVVTVAVYLMKTYGGIDCIPTIGDRF---------- 234 Query: 248 NGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTK 307 I LP V+P L W++I+ L P A ++A+LGAIESLL A V DG+ G + Sbjct: 235 -TIKSELPDAVVP--------ALDWEAIKNLFPVAITIAVLGAIESLLSATVADGVIGDR 285 Query: 308 HKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVL 367 H +N+EL+ QG NI+AP FGGI AT AIAR+ N+ G +PI+ +IH+I+++L LL L Sbjct: 286 HDSNTELIAQGAANIVAPLFGGIPATGAIARTMTNINNGGKTPIAGIIHAIVLLLILLFL 345 Query: 368 APLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAI 427 PL ++P++ +A +L++V++NMS +V L PK D+ V+L+ LTV+FD+ +AI Sbjct: 346 MPLAQYIPMACLAGVLVIVSYNMS-GWRVFKALLKNPKSDVTVLLITFFLTVIFDLTVAI 404 Query: 428 SVGIVLASLLFMRRIARMTRLAPVV-----------------VDVPDDVLVLRVIGPLFF 470 VG+++A +LFM+R+ T ++ + + +P V V + GP FF Sbjct: 405 EVGLIIACVLFMKRVMETTEISVITDEIDPNKESDIAVNEENIMIPKGVEVYEITGPYFF 464 Query: 471 AAAEGLFTDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVK-RLPEGCELRVCNVEFQ 529 A + + + I++ VP +D+ G+ + E + + V + Sbjct: 465 GIATKFEETMAQLGDRPNVRIIRMRKVPFIDSTGIHNLTTLCEMSQKEKITVILSGVNEK 524 Query: 530 PLRTMARAGIQPIPGRLAFFPNRRAAM 556 + + ++G + G+ PN + A+ Sbjct: 525 VYKVLEKSGFYELLGKENICPNFKIAL 551 Lambda K H 0.328 0.142 0.425 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: 638 Number of extensions: 26 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: 559 Length of database: 559 Length adjustment: 36 Effective length of query: 523 Effective length of database: 523 Effective search space: 273529 Effective search space used: 273529 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 (21.7 bits) S2: 53 (25.0 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