Align Citrate:H+ symporter (characterized)
to candidate Pf6N2E2_1184 L-Proline/Glycine betaine transporter ProP
Query= TCDB::P16482 (444 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1184 Length = 434 Score = 257 bits (656), Expect = 6e-73 Identities = 144/428 (33%), Positives = 230/428 (53%), Gaps = 9/428 (2%) Query: 23 GGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMR 82 G R +L V+ G LE FDF LF ++ IA FFPAS SL+ ++ GF+ R Sbjct: 5 GRERRKLVLAVSVGAALEWFDFTLFAIFSLQIAAAFFPASDPLMSLLASYLALAVGFVAR 64 Query: 83 PIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGF 142 P+GA+++G Y D+ GR+ L +++ +M GT +I + P+Y+TIG WAPL V++ R+LQG Sbjct: 65 PLGALLMGRYADRQGRKAALTLSIMLMGAGTLIIAVCPTYETIGWWAPLSVVVARILQGV 124 Query: 143 SAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWG 202 +AG E+GG YL E A R+ + S Q +Q + ++ L++ L P+ + +WG Sbjct: 125 AAGGEIGGALAYLVETAPADRRALFASSQQVAQAGSFLLCGLSASLLSSALTPAQLDEWG 184 Query: 203 WRIPFLFGVLIVPFIFILRRKLEETQ---EFTARRHHLAMRQVFATLLANWQVVIAGMMM 259 WR+P++FG+L+V +RR LEE++ F + AM +L ++ G+++ Sbjct: 185 WRVPYVFGLLVVVAGLKIRRSLEESEPLRRFLDNQDKHAMAGKGPSLRPYLPNLVMGVLI 244 Query: 260 VAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSV 319 V + T A LI + PT+ VL L + + L +LV + P+ LSDR GR +V Sbjct: 245 VVLWTVATQLIN-FIPTYASMVLELPRNKAYLGLVLVGLITLL-CPLTALLSDRIGRYTV 302 Query: 320 LIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRV 379 ++ + A+P L N+PS ++ L+ + +Y G AL E+ P +VR Sbjct: 303 MLIGAVGVALCAYPGFVWLNNSPSLQTLIIFQCALAVLMVLYTGPAAAALAELFPVQVRA 362 Query: 380 AGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYL----YRR 435 G SLAY+L+ +FG TP + T + +GD + +W+ AA + ++ YR Sbjct: 363 LGVSLAYALSVTLFGSATPALITLIYRQSGDALAAAHWLFAAACLSAIPLAWVSLSKYRA 422 Query: 436 SAVALQTA 443 SA TA Sbjct: 423 SATPALTA 430 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: 508 Number of extensions: 25 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: 444 Length of database: 434 Length adjustment: 32 Effective length of query: 412 Effective length of database: 402 Effective search space: 165624 Effective search space used: 165624 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