Align citrate transporter (characterized)
to candidate HSERO_RS15670 HSERO_RS15670 major facilitator transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS15670 Length = 427 Score = 296 bits (759), Expect = 6e-85 Identities = 166/410 (40%), Positives = 245/410 (59%), Gaps = 9/410 (2%) Query: 13 AILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVV 72 AI+ + GN LE FD ++G +A IAK FFP + +L+LTFA FG F MRP+GAVV Sbjct: 20 AIISSSIGNALEWFDILIYGAFAVVIAKQFFPTGDDSVSLLLTFATFGVSFFMRPLGAVV 79 Query: 73 LGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVEL 132 LGAY DR GR+ LM+++ +M GT +IA +P Y +IGLLAP + +G+++QGFSAG E Sbjct: 80 LGAYSDRAGRKAALMLSIMLMTVGTAMIAFMPSYASIGLLAPAGIALGKMIQGFSAGGEF 139 Query: 133 GGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFF 192 G + +L E A P +GF++SWQ ASQ +++++AAL G LN L ++++ WGWR+PF Sbjct: 140 GSSTAFLVEHA-PHRRGFFSSWQVASQGISLLLAALFGAVLNNMLTPEQLASWGWRVPFI 198 Query: 193 IGCMIIPLIFVLRRSLQETEAFLQRKHRPDT--REIFTTIAKNWRIITAGTLLVAMTTTT 250 G +I P +RR L E F + + + R+ F K +I AG++++A T Sbjct: 199 FGLLIAPAGIYIRRHLDEAPEFKESSEKTNAPLRDTFAH-QKMRLLIGAGSVIMA---TV 254 Query: 251 FYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLMGITLL 310 ++++Y PTY L L A S + G+ FI P+ GA+SD+IGR P ++ + L Sbjct: 255 SVYLSLYIPTYAVKQLGLPAWSSFAAMSVAGLIMFIGSPLVGALSDKIGRTPFMITSSAL 314 Query: 311 ALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAF 370 +V T P+ +LT +P F ++ L+ MY AM A L ++ PV R G SLA+ Sbjct: 315 YIVLTYPMFVFLTNSPGFLQLLLLQTVIGVLMTMYFAAMPALLADIFPVATRGTGMSLAY 374 Query: 371 SLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLFARL 420 ++A IFGG I T L+ TGDK S ++++ A+ L A+ L ARL Sbjct: 375 NIAVTIFGGFAGLIITWLIDFTGDKLSVSYFVIFGAVLSLIAS--LSARL 422 Lambda K H 0.328 0.141 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: 482 Number of extensions: 23 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: 431 Length of database: 427 Length adjustment: 32 Effective length of query: 399 Effective length of database: 395 Effective search space: 157605 Effective search space used: 157605 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