Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Pedo557:CA265_RS10595 Length = 458 Score = 261 bits (667), Expect = 3e-74 Identities = 144/376 (38%), Positives = 231/376 (61%), Gaps = 15/376 (3%) Query: 39 LGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVV 98 L D F++LIKM++AP++F T+V G+A + ++K+VG+ GG L +F +S ++L++G+V+V Sbjct: 92 LSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMSLVLGMVLV 151 Query: 99 NVVQPGNGMHIDVSTLDASKVAAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMF 158 N+ +PG H+ +S D A S+ FI +V P +I + + +ILQ+++F Sbjct: 152 NLFEPGR--HMKLSLPDQLVNTGIQKAA--MSVKDFIAHVFPKSIAESMSTNEILQIVVF 207 Query: 159 SVIFGFALHRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSL 218 S+ FG A +G G+ V+ D AHV+ + +M AP+ GAM + G+ L Sbjct: 208 SLFFGVATAAIGDLGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAIVAKQGLNVL 267 Query: 219 VQLGQLMICFYITCVLFVLVVLGAICRAHGFSVLK-----LIRYIREELLIVLGTSSSES 273 + FY+ L +L A+ GF VLK L+ ++E L+ T+SSE+ Sbjct: 268 NTYAIFIGEFYLG-----LAILWAVLIFLGFLVLKKRIFRLVNDMKEPALLAFSTASSEA 322 Query: 274 ALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQIT 333 A P+ ++ +ER G K +V V+P GYSFNLDG+ +Y+T A++FIAQA H+ QI+ Sbjct: 323 AYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAYGIHLGFEQQIS 382 Query: 334 LLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGN 393 +LL+L+L+SKG AGV + +V+A T+++ ++P AGLAL++GID + R+ TN+VGN Sbjct: 383 MLLILMLTSKGIAGVPRASLVVIAGTIASF-NIPEAGLALLIGIDPLLDMGRSATNVVGN 441 Query: 394 AVATVVVAKWVKELDE 409 ++AT VV+KW EL E Sbjct: 442 SIATAVVSKWEGELKE 457 Lambda K H 0.326 0.142 0.402 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: 458 Number of extensions: 21 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: 444 Length of database: 458 Length adjustment: 33 Effective length of query: 411 Effective length of database: 425 Effective search space: 174675 Effective search space used: 174675 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 (21.6 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