Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Korea:Ga0059261_0201 Length = 455 Score = 272 bits (695), Expect = 2e-77 Identities = 156/383 (40%), Positives = 226/383 (59%), Gaps = 8/383 (2%) Query: 41 FVKLIKMIIAPVIFCTVVTGIAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQ 100 F++LIKMIIAP++F T+V GIA M A+GR G A+ +F S ++L +GLI+VN+ Q Sbjct: 56 FLRLIKMIIAPLVFATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQ 115 Query: 101 PGAGMNVDPATLDAKA-VAVYADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVL 159 PG G+N +DA + V A KD F V PAS I A A ILQ+++F++ Sbjct: 116 PGVGLNFPLPPVDATSGVEKAAFNLKD-----FFTHVFPASGIEAMAKNEILQIVIFSLF 170 Query: 160 FGFALHRLGSKGQLIFNVIESFSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQL 219 G A+ +G K + + + +E+ V+ + N +MR API F A+A T+ + G + L Sbjct: 171 IGVAITAVGEKAKPLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIGNL 230 Query: 220 GQLIICFYITCILFVVLVLGSIAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDK 279 + FYI L++G G +RYIR+ LL+ T+SSE+A PR L+ Sbjct: 231 AYFMGTFYIAMFTLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTLEA 290 Query: 280 MEKLGCRKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLS 339 +++ G + V+P GYSFNLDG+ IY+T A +FIAQA + + +IT+L+VL+++ Sbjct: 291 LDRFGVPPRIASFVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLMIT 350 Query: 340 SKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVA 399 SKG AGV + +V+AATL +P AGL LILGID F+ R+ TN+VGN VA+ VVA Sbjct: 351 SKGIAGVPRASLVVIAATLGFF-DIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAVVA 409 Query: 400 KWV-KELDHKKLDDVLNNRAPDG 421 KW LD + D+ AP G Sbjct: 410 KWEGGRLDPIEPADIEPPHAPTG 432 Score = 25.4 bits (54), Expect = 0.004 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 10/92 (10%) Query: 12 QVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMII---------APVIFCTVVTGIA 62 ++L + + +G +GE+ KPL L+ +++ AP+ V G Sbjct: 160 EILQIVIFSLFIGVAITAVGEKAKPLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTL 219 Query: 63 GMESMKAVGRTG-AVALLYFEIVSTIALIIGL 93 +G + Y + + AL+IG+ Sbjct: 220 AERGPAIIGNLAYFMGTFYIAMFTLWALLIGV 251 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: 502 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 428 Length of database: 455 Length adjustment: 32 Effective length of query: 396 Effective length of database: 423 Effective search space: 167508 Effective search space used: 167508 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