Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate RR42_RS16025 RR42_RS16025 sulfate transporter
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Cup4G11:RR42_RS16025 Length = 596 Score = 348 bits (893), Expect = e-100 Identities = 217/581 (37%), Positives = 314/581 (54%), Gaps = 68/581 (11%) Query: 24 YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83 Y A F +DL AG+TVG++A+PLAMA AI SG+ PQ GL+TA +AG +IA GGS + Sbjct: 21 YNRALFFKDLAAGLTVGVVALPLAMAFAIASGMPPQAGLFTAIIAGFLIAALGGSPVQIG 80 Query: 84 GPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGI 143 GP AF+VI+Y + ++G+A LL+AT+L+G L MGL R G LI +IPV++ +GFT+GI Sbjct: 81 GPAGAFIVIVYGIVARYGVANLLIATILAGGLLFAMGLFRLGTLIRFIPVAIVIGFTNGI 140 Query: 144 GITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLG 203 + I QI DFLGLQ +P ++L ++ L ALPT++ A+ + +L ++ W RL Sbjct: 141 AVLIMVSQIADFLGLQTGKLPGNFLSQMRVLGRALPTVSWPTVALAVSSLVVVAGWSRLA 200 Query: 204 I-------------------------------RLPGHLPALLAGCAVMGIVNLLGGHVAT 232 + +PG + AL+ A G+++L V T Sbjct: 201 LLAGKRWRPVSTVAANPANPPNAHGRLGRALAMVPGTVIALVLATAANGLLHL---PVET 257 Query: 233 IGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIE 292 IG++F GIPQ LP LP L+W ++ L+ ++A+LGAIE Sbjct: 258 IGTRF----------GGIPQGLPPFALP--------QLSWQLVQQLVAPTLTIALLGAIE 299 Query: 293 SLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPIS 352 SLLCA V D + +H N EL+ QG+ NI+ PFFGG+ AT IAR+ NVR+G +P++ Sbjct: 300 SLLCARVADSLIDDRHDPNQELMAQGIANIVTPFFGGLPATGTIARTVTNVRSGGRTPVA 359 Query: 353 AVIHSILVILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKV-VDLLRHAPKDDIIVM 411 +IH+ ++L +LV APL S +PL+ +AA+LL VAWNM E H + L+ + I++ Sbjct: 360 GMIHAATLLLIVLVAAPLASAIPLATLAAILLYVAWNMGEWHMFGLTHLKRYSNNYRIIL 419 Query: 412 LLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMTR---LAPVVVDVPDD--------VL 460 L LTV+FD+ +A+ VG+VLA L F+ R+A +T+ +AP + D V Sbjct: 420 LGTFVLTVVFDLTVAVQVGLVLACLFFIYRMAALTQIEAIAPAALPPAADGRPLPAGEVA 479 Query: 461 VLRVIGPLFFAA---AEGLFTDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLP- 516 + G LFF A E L + ++IL + LD GLD K L Sbjct: 480 AYHMTGALFFGAVNKVEALIDPRDRTQPVPAVLILDVGKLVALDTTGLDTLDALRKTLAR 539 Query: 517 EGCELRVCNVEFQPLRTMARAGIQPIPGRLAFFPNRRAAMA 557 G L +C Q + M RAG G + AA A Sbjct: 540 RGGTLVICAAPAQVMSLMRRAGFLEQMGTANYCDTLAAACA 580 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: 719 Number of extensions: 37 Number of successful extensions: 4 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: 596 Length adjustment: 36 Effective length of query: 523 Effective length of database: 560 Effective search space: 292880 Effective search space used: 292880 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