Align Solute carrier family 13 member 5; Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter (characterized)
to candidate WP_086511848.1 BZY95_RS21045 SLC13 family permease
Query= SwissProt::Q86YT5 (568 letters) >NCBI__GCF_002151265.1:WP_086511848.1 Length = 532 Score = 275 bits (702), Expect = 4e-78 Identities = 167/500 (33%), Positives = 255/500 (51%), Gaps = 46/500 (9%) Query: 44 LMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERW 103 LMA++W TE IPL+ T+L+P++L P+ Q Y LFLGG ++A+A+E+W Sbjct: 64 LMAVWWMTEAIPLSATALLPIVLIPMLTERTVAQATAPYASSIVFLFLGGFLIAIAMEKW 123 Query: 104 NLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQM-EAT 162 NLH+RIAL TL VG P R++LG M T LSMW+SNTATT MM+PI ++L + E + Sbjct: 124 NLHRRIALLTLARVGVSPHRIVLGMMLATGFLSMWVSNTATTLMMLPIGLSVLALVAERS 183 Query: 163 SAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTA 222 +TE D +A V F D+ KR + L I ++AS+GG Sbjct: 184 GESTETVTADHDHHRA-----GHVDFIA-------DENIKRFGLCLLLAIAWSASMGGLG 231 Query: 223 TLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFK 282 TL G+ PN ++ G + + + F W P +L W+ + V F + Sbjct: 232 TLLGSPPNAIVAGYAADELGRN---IGFLDWMLLGVPLAFTFILVGWVLMTRVLYPFKVE 288 Query: 283 KSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWL 342 + G ++++ E RKLG L+ E VL+ F LW PG + Sbjct: 289 EIPG-----------GQEMIEGEARKLGSLTQGEKMVLLVFGSAAFLWVV--PGVLGNIP 335 Query: 343 TVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVT 402 V G + D +A+ LF++P+ R + E +L+WK Sbjct: 336 GVGQWLGPLGNLDDTAIAVAAGIALFVLPA-------RGRNEM----------VLNWKDA 378 Query: 403 QEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTEC 462 ++ +PWG++LL GGG +LA +GL W G+Q+ L +P + ++ +V TE Sbjct: 379 EDGLPWGVLLLFGGGLSLAGAVAGTGLDSWFGQQITGLGVLPILLLVAAVATIVLFLTEV 438 Query: 463 TSNVATTTLFLPIFASMSRSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKV 522 TSN AT F+P+ ++ IG + + +++P +A+ AFMLPV TPPNAIVF G + + Sbjct: 439 TSNTATAATFIPVLGGVAVGIGTDSMTLLIPAAFAATCAFMLPVGTPPNAIVFGTGAVSI 498 Query: 523 ADMVKTGVIMNIIGVFCVFL 542 M + GV++NIIG+ + L Sbjct: 499 GQMARGGVVLNIIGIVLITL 518 Lambda K H 0.327 0.139 0.436 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: 875 Number of extensions: 47 Number of successful extensions: 8 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: 568 Length of database: 532 Length adjustment: 36 Effective length of query: 532 Effective length of database: 496 Effective search space: 263872 Effective search space used: 263872 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 Apr 09 2024. 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