Align Citrate:H+ symporter (characterized)
to candidate RR42_RS27250 RR42_RS27250 citrate-proton symporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS27250 Length = 428 Score = 633 bits (1632), Expect = 0.0 Identities = 308/417 (73%), Positives = 359/417 (86%) Query: 20 ATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGF 79 A G +++GA+LRVTSGNFLEQFDFFLFGFYATYIAHTFFP++SEFASLM+TFAVFGAGF Sbjct: 5 AVPGSSKLGAVLRVTSGNFLEQFDFFLFGFYATYIAHTFFPSNSEFASLMLTFAVFGAGF 64 Query: 80 LMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLL 139 LMRP+GAI+LGAYID+VGRRKGLIVTLS+MA+GT LI L+P Y +IG+ AP+LVLIGRLL Sbjct: 65 LMRPLGAILLGAYIDEVGRRKGLIVTLSLMASGTILIALVPGYASIGVLAPVLVLIGRLL 124 Query: 140 QGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAIS 199 QGFSAGAELGGVSVYLAE+ATPG KGFYT+WQS SQQ+AI+VAA +GF LN L + Sbjct: 125 QGFSAGAELGGVSVYLAEMATPGHKGFYTAWQSASQQIAIVVAAGLGFGLNYWLTTDELG 184 Query: 200 DWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANWQVVIAGMMM 259 WGWRIPF G LIVPF+F+LRR L+ET+ F RRHH + R+VF ++L NW+ V+AGM++ Sbjct: 185 AWGWRIPFFIGCLIVPFLFVLRRSLQETEAFRTRRHHPSTREVFDSMLGNWRTVLAGMLL 244 Query: 260 VAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSV 319 VAMTTT FYLITVY PTFGK VL LS +DSL VTL V ISNF WLP+GGALSDR GRR + Sbjct: 245 VAMTTTTFYLITVYTPTFGKTVLKLSTADSLGVTLCVGISNFIWLPIGGALSDRIGRRPI 304 Query: 320 LIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRV 379 L+A++ +AL TA+PAL+ LA APSF ML VLLWLSF++GMYNGAM+ ALTE+MP EVRV Sbjct: 305 LLAISAIALVTAYPALSWLAGAPSFGRMLIVLLWLSFLFGMYNGAMVVALTEVMPVEVRV 364 Query: 380 AGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYLYRRS 436 AGFSLAYSLATAVFGGFTP +ST LIE TGDKA+PGYWMSFAA CGLLAT LYR++ Sbjct: 365 AGFSLAYSLATAVFGGFTPAVSTYLIEVTGDKAAPGYWMSFAAACGLLATLILYRKA 421 Lambda K H 0.329 0.139 0.421 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: 739 Number of extensions: 27 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: 444 Length of database: 428 Length adjustment: 32 Effective length of query: 412 Effective length of database: 396 Effective search space: 163152 Effective search space used: 163152 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 (21.9 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