Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_01363 H281DRAFT_01363 aerobic C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_01363 Length = 433 Score = 489 bits (1260), Expect = e-143 Identities = 241/419 (57%), Positives = 320/419 (76%) Query: 2 KTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGI 61 K +++LYF V AI IG+LLGHF P + +MKPLGD F+KLIKM+I P+IFCTVVTGI Sbjct: 15 KKPFYRTLYFHVFAAIIIGVLLGHFAPSLAVKMKPLGDAFIKLIKMVIGPIIFCTVVTGI 74 Query: 62 AGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYA 121 AGM MK VGR G ALLYFEIVST++L+IGL+ ++ PG+G N+DPAT+D KA+A Y Sbjct: 75 AGMGDMKKVGRVGGKALLYFEIVSTLSLVIGLVAGHIFHPGSGFNLDPATIDTKALAGYT 134 Query: 122 DQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESF 181 A Q V F+M +IP +V GAFASGN+LQ+LL +VLFG AL G +G+ + +I+ F Sbjct: 135 TAAHQQNTVEFLMHIIPDTVTGAFASGNVLQILLISVLFGAALAATGERGRPLIAMIDYF 194 Query: 182 SQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSI 241 + FGI+++IM++A IGAFG++AFTIG YG+G +V L +LI FY T +FV++VLG+I Sbjct: 195 AHTFFGIVHIIMKVAAIGAFGSIAFTIGTYGIGAVVPLLKLIGAFYATLAVFVIVVLGAI 254 Query: 242 AKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFN 301 ++ GFSIF+F+ YIREE+LIVLGTSSSE+ALP+ML+K+E+LGC KSVVGLVIP GYSFN Sbjct: 255 SRLLGFSIFRFMSYIREEILIVLGTSSSEAALPQMLEKLERLGCSKSVVGLVIPAGYSFN 314 Query: 302 LDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAV 361 LDGT+IYLTMA +FIAQA N ++ + Q+TL+ V +L+SKGA+GV G+ F++L +TL Sbjct: 315 LDGTNIYLTMAVLFIAQAFNIELSLTQQLTLVGVAMLTSKGASGVAGAAFVMLTSTLLVF 374 Query: 362 GHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420 +PV+G+ LILGI RFM A+ N +GNGVAT+VV+ W ELD KL+ ++ R D Sbjct: 375 PLIPVSGMVLILGIHRFMGTGLAIANTIGNGVATLVVSAWEHELDRSKLNAGMSRRRAD 433 Lambda K H 0.327 0.142 0.401 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: 600 Number of extensions: 24 Number of successful extensions: 1 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: 428 Length of database: 433 Length adjustment: 32 Effective length of query: 396 Effective length of database: 401 Effective search space: 158796 Effective search space used: 158796 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: 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