Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 8500834 DvMF_1575 sulfate transporter (RefSeq)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Miya:8500834 Length = 570 Score = 385 bits (990), Expect = e-111 Identities = 228/544 (41%), Positives = 322/544 (59%), Gaps = 39/544 (7%) Query: 24 YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83 Y+ +F RDL+AG+TVG++A+PLAMA AI SG P+ GL+TA VAG +I+L GGSR+ + Sbjct: 26 YSTQKFIRDLLAGLTVGVVALPLAMAFAIASGTTPERGLFTAIVAGFLISLLGGSRYQIG 85 Query: 84 GPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGI 143 GPT AFVVI+Y V + G GL++ TLL+G L++ GL R G LI+YIP VT GFT+GI Sbjct: 86 GPTGAFVVIIYNVIYRHGYDGLVITTLLAGAMLLIFGLCRIGVLIKYIPYPVTTGFTAGI 145 Query: 144 GITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLG 203 + I + Q+KDF GLQM VP + K A L TIN + + L ++ R Sbjct: 146 AVLIFSSQMKDFFGLQMDAVPPEFFDKWLAYAEHLGTINTTTLCVAGLALACILATRRF- 204 Query: 204 IRLPGHLPALLAGCAVMGI-VNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWD 262 +P +PA + G AV + V LG V TIGS+F GIP+ LP V P Sbjct: 205 --IP-RIPAPVVGVAVASLAVWALGLQVETIGSRF----------GGIPRELPSFVWP-- 249 Query: 263 LPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNI 322 T T+ +R LLP A ++A+L IESLL VV DGMTG KH +N EL QG+ NI Sbjct: 250 ------TFTFARVRELLPDAMTIALLAGIESLLSCVVADGMTGDKHNSNVELTAQGVANI 303 Query: 323 IAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAAL 382 + FGGI AT AIAR+ N+R+G +P++ ++H+ +++ +L LAPL S++PL+++AA+ Sbjct: 304 ASVLFGGIPATGAIARTVTNIRSGGQTPVAGMVHAAVLVAFVLFLAPLASFIPLASLAAV 363 Query: 383 LLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRI 442 L+MV+W+MSE HK + LLR APK DI VM L LTV+ D+ +A+ VG++LASLLFMRR+ Sbjct: 364 LIMVSWDMSELHKFLRLLR-APKSDITVMCLTFVLTVVIDLTVAVYVGVMLASLLFMRRM 422 Query: 443 ARMTRLAPVVVD--------------VPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKR 488 + +T + +D VP+ V V + GP FF A+ + ++ + Sbjct: 423 SEVTAICSCAIDDKPVIQGRETAELVVPEGVQVYEIDGPFFFGVADRFQSVSQALQKQPE 482 Query: 489 IVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQPIPGRLA 547 + IL+ +D+ G +A + F + G L + V R M R G + GR Sbjct: 483 VFILRMRKASTVDSTGANALEAFCRTCRRRGTVLLLSGVRPAARRMMERFGTLDLIGREN 542 Query: 548 FFPN 551 F N Sbjct: 543 LFEN 546 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: 668 Number of extensions: 36 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: 570 Length adjustment: 36 Effective length of query: 523 Effective length of database: 534 Effective search space: 279282 Effective search space used: 279282 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 Apr 09 2024. 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