Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Caulo:CCNA_00264 Length = 417 Score = 294 bits (752), Expect = 4e-84 Identities = 175/423 (41%), Positives = 262/423 (61%), Gaps = 37/423 (8%) Query: 9 AWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAG------------DIFIHLIKMIV 56 A+ I+ +M+LG+L+G W L PAG DIF+ LIKMI+ Sbjct: 6 AYLIIASMILGVLVG-----------WTCNQFLDPAGAKSAADNLSIITDIFLRLIKMII 54 Query: 57 VPIVISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQ 116 P+V +TLV G+A + DA +GRIGAKT+ +F + V+++LG+ + ++ PGAG++M Sbjct: 55 APLVFTTLVAGVAHMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNM-- 112 Query: 117 LATVDIS-KYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLS 175 A VD++ K +TT+A + G I LVPT+I +MAK E+L I+ FS+ G ++ Sbjct: 113 -AHVDVAMKTTATTDAFT-----LKGFITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVA 166 Query: 176 SLPATHREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVL 235 +L + L V ++ ++ M KVT VM+ AP+ +FA +A T+A G L K VL Sbjct: 167 ALDDKAPQILELVEQA-AQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVL 225 Query: 236 LVHFA--ILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEA 293 + A +L+ L + G++ + G V L +++D ++LA+STASSE+ PRI++ + Sbjct: 226 GFYSAMGVLWALLFIAGLL--VLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPK 283 Query: 294 YGAPVSITSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKG 353 G I SFV+P GYSFNLDGS LY + A +FI Q +G++L++ Q+I ++L LMVTSKG Sbjct: 284 VGVRRRIVSFVLPLGYSFNLDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKG 343 Query: 354 IAGVPGVSFVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEH 413 IAGVP S VV++ATL G+P +A + GVD +LDM R+A NVVGN++A V+AKWE Sbjct: 344 IAGVPRASLVVIMATLTYFGLPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEG 403 Query: 414 KFD 416 + D Sbjct: 404 ELD 406 Lambda K H 0.326 0.141 0.403 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: 464 Number of extensions: 17 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: 437 Length of database: 417 Length adjustment: 32 Effective length of query: 405 Effective length of database: 385 Effective search space: 155925 Effective search space used: 155925 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