Align Ectoine/proline transporter ProP (characterized)
to candidate AO353_26710 AO353_26710 citrate-proton symporter
Query= SwissProt::Q79VC4 (504 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26710 Length = 434 Score = 211 bits (536), Expect = 5e-59 Identities = 133/426 (31%), Positives = 214/426 (50%), Gaps = 21/426 (4%) Query: 32 AIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGGLV 91 AI GNF+E +DF ++G+ + A F + L+ F +L+RPLG ++ Sbjct: 18 AIFRVTSGNFLEQFDFFLFGFYATYIAAAFFPASSEFASLMMTFAVFGAGFLMRPLGAVI 77 Query: 92 LGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEY 151 LG D VGR+K L VT+++MA T LI L+P +IG +A L+ + +++QGFS G E Sbjct: 78 LGAYIDDVGRRKGLIVTLSIMASGTILIVLVPGYETIGLFAPALVLIGRLLQGFSAGAEL 137 Query: 152 AGATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASV-VAITTWVTTHFYGATAMEDFGW 210 G + Y+AE A R+GFF ++ + A++ A+ W+ AT + D+GW Sbjct: 138 GGVSVYLAEIATPGRKGFFTSWQSASQQVAIVVAAALGYALNQWMP-----ATVVADWGW 192 Query: 211 RIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWR 270 RIPF + LR + ET F + P + + G + +W+ Sbjct: 193 RIPFFVGCMIVPFIFLLRRSLEETAEFTARRHRP------------SMRQVFGTLLQNWQ 240 Query: 271 PLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWS 330 ++ G+ +VA T TA Y +T Y P + + + L ++ A VT+ + V LP G S Sbjct: 241 IVIAGMLMVALTTTAFYLITVYAPTFGKTVLHLSTSDALLVTLLVGVSNFCWLPLGGALS 300 Query: 331 DRVGRKPVYATAVAATLILMVPA--FLIMNTGTIGAVLIALSMVAIPTGLYVALSASALP 388 DR+GR+PV TL PA +L+ I +L+ L + I GLY +AL Sbjct: 301 DRIGRRPVLVAMTLLTLATAYPALTYLVQAPSFINMLLVLLWLSFI-YGLYNGAMVAALT 359 Query: 389 ALFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALL 448 + P R +G ++Y+++ ++FGG TP I+ FL+Q +G P ++ F + A A L Sbjct: 360 EIMPVEVRVAGFSLAYSLATAVFGGFTPAISTFLIQYSGDKAAPGYWMSFAALCALCATL 419 Query: 449 FMTESS 454 ++ S Sbjct: 420 YLYRRS 425 Lambda K H 0.322 0.138 0.407 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: 578 Number of extensions: 37 Number of successful extensions: 4 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: 504 Length of database: 434 Length adjustment: 33 Effective length of query: 471 Effective length of database: 401 Effective search space: 188871 Effective search space used: 188871 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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