Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate PfGW456L13_3155 L-Proline/Glycine betaine transporter ProP
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3155 Length = 429 Score = 234 bits (597), Expect = 4e-66 Identities = 145/417 (34%), Positives = 218/417 (52%), Gaps = 7/417 (1%) Query: 23 GNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGSGFLMRPVGAIVLGAYIDR 82 GNF+E FDF ++GF AT IA+ FFP+ A+L+ TFAVF F RP+G I G DR Sbjct: 8 GNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVFAVAFAFRPLGGIFFGMLGDR 67 Query: 83 IGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGRLLQGFSAGVELGGVSVYL 142 IGR++ L +T+ +M T LI L+P Y IG+ AP L+ L R QGFSAG E G YL Sbjct: 68 IGRKRTLAMTILLMAGATTLIGLLPTYAAIGVMAPILLSLIRCAQGFSAGGEYAGACAYL 127 Query: 143 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDAISEWGWRIPFFIGCMIIP 202 E A + +Y S+ S A AA++ Y+L +L +A+ WGWR+PF I + Sbjct: 128 MEHAPSDKRAWYGSFIPVSTFSAFAAAAVVAYALEASLSAEAMGSWGWRLPFLIAAPLGL 187 Query: 203 LIFVLRRSLQETEAF--LQRKHRPDTREIFATIAKNWRIITAGTLLVAMTTTTFYFITVY 260 + LR L ET AF + ++H + T+ + I V++T +FY T Y Sbjct: 188 VGLYLRWKLDETPAFQAVTQEHAVAHSPLKETLRNHGAAICCLGAFVSLTALSFYMFTTY 247 Query: 261 TPTYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDRIGRRAVLMGITLLALITTWP 320 TY + LS +L+V+++ + P+ G SDR+GRR +M L ++ +P Sbjct: 248 FATYLQVAGGLSRATALLVSLIALLFAAAICPLAGLYSDRVGRRVTVMTACALLIVVVYP 307 Query: 321 VMQWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAA-LTEVMPVYVRTVGFSLAFSLATAI 379 +L A+ ++V + + G + AA L+E P R ++ +++A + Sbjct: 308 --SFLMASSGSFAASIVGVMLLAIGAVLCGVVTAALLSETFPTRTRYTASAITYNMAYTL 365 Query: 380 FGGLTPAISTALVKLTGDKSSPGWWLMCAALCGLAATAML--FVRLSRGYIAAENKA 434 FGG P ++T L+ TG SP ++L+ AL LA L R+S +AA+ KA Sbjct: 366 FGGTAPLVATWLISTTGSNLSPAFYLIAIALLALAGGLALPETSRISLHDVAAQEKA 422 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: 470 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: 434 Length of database: 429 Length adjustment: 32 Effective length of query: 402 Effective length of database: 397 Effective search space: 159594 Effective search space used: 159594 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: 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