Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate WP_013459347.1 SULKU_RS02455 MFS transporter
Query= SwissProt::P0A2G3 (434 letters) >NCBI__GCF_000183725.1:WP_013459347.1 Length = 409 Score = 182 bits (463), Expect = 1e-50 Identities = 112/401 (27%), Positives = 197/401 (49%), Gaps = 26/401 (6%) Query: 23 GNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGSGFLMRPVGAIVLGAYIDR 82 GN +E +DF L GF A + FFP+ F SL+ +F F +G +MRPVGA++ G DR Sbjct: 14 GNVIEYYDFALIGFLAVMMGNLFFPSHDPFLSLLGSFGAFAAGMIMRPVGALIFGHIGDR 73 Query: 83 IGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGRLLQGFSAGVELGGVSVYL 142 + RR LM +L +M T LI +P Y IG+ AP L++L R++QG S G E VYL Sbjct: 74 VSRRTALMSSLLMMALPTFLIGFLPTYAQIGILAPILLVLLRMIQGLSVGGEYASSIVYL 133 Query: 143 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDAISEWGWRIPFFIGCMIIP 202 E + P ++ Y S+ S ++ + + + +L +G DA+ EWGWRIPF+ +I Sbjct: 134 VEQSAPDHQNLYGSFVSVGAKIGMALGSGFCGALLWYIGGDAMGEWGWRIPFWASIIIAA 193 Query: 203 LIFVLRRSLQETEAFLQRKHRPDTREIFATIAKNWRIITAGTLLVAMTTTTFYFITVYTP 262 LRR+L + + K P + + W+ +T + + +Y + +Y P Sbjct: 194 AGLYLRRNLTDDYRPSEDKTVPIVAILRHHRREFWQFLTIASAIWVF----YYTVFIYLP 249 Query: 263 TYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDRIGRRAVLMGITLLALITTWPVM 322 + LS ++ + L V +++P+ ++D IG ++ ++ I+ +P+ Sbjct: 250 IWLEGSAGLSKAEAGQINTLSIVVGVVFIPLMAMVADVIGSLRLMRLTSITLAISVYPLF 309 Query: 323 QWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTV------GFSLAFSL- 375 W++ + + + G ++ P++ TV G+ +F+ Sbjct: 310 YWMSIGGFWGALAGTI-----------GLVILLCAFQAPIFASTVNALHYHGYRASFTAV 358 Query: 376 ----ATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCG 412 A I GG+TPA+ T++ + +G+ +P + + A+L G Sbjct: 359 ILGSAAGIVGGITPALMTSITEYSGNPFAPSYLIAAASLMG 399 Lambda K H 0.329 0.140 0.432 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: 471 Number of extensions: 20 Number of successful extensions: 3 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: 434 Length of database: 409 Length adjustment: 32 Effective length of query: 402 Effective length of database: 377 Effective search space: 151554 Effective search space used: 151554 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 (21.8 bits) S2: 50 (23.9 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