Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate PfGW456L13_635 Uncharacterized transporter, similarity to citrate transporter
Query= TCDB::P42308 (426 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_635 Length = 435 Score = 556 bits (1433), Expect = e-163 Identities = 267/427 (62%), Positives = 345/427 (80%), Gaps = 5/427 (1%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 ML LGF M+I FM+LIM+ RLSALIALI++PI+FAL GF +G MM++G+T LAPTG Sbjct: 1 MLTFLGFAMVITFMFLIMTKRLSALIALIIIPIIFALFGGFSPKIGPMMLEGITKLAPTG 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +ML+FAILYF +MIDSGLFDP + KIL VKGDPLK++VGTAVL + +SLDGDG TTYMI Sbjct: 61 VMLMFAILYFALMIDSGLFDPAVRKILKLVKGDPLKVSVGTAVLALVVSLDGDGATTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180 +AAMLPLY R+GM+ ++AG+ +L GVMN+ PWGGPTAR ++L +D S++F P+IPA Sbjct: 121 CVAAMLPLYSRIGMSPRIMAGLIILAGGVMNMTPWGGPTARAASALHVDPSDIFVPMIPA 180 Query: 181 MIAGILWVIAVAYILGKKERKRLGVI-----SIDHAPSSDPEAAPLKRPALQWFNLLLTV 235 M+AG++ ++ +AY GK+ER RLG + IDH+ S + +RP L WFN LT+ Sbjct: 181 MLAGVVAILVIAYFYGKRERARLGELHLVGDEIDHSEISVSQFPDARRPKLIWFNGALTL 240 Query: 236 ALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIFT 295 ALM LI LLPLPVLFM AF++A++VNYP +++Q+ R++AHAG+ L VV ++FAAGIFT Sbjct: 241 ALMCTLIAGLLPLPVLFMVAFSIAMIVNYPCLQQQKDRVAAHAGSVLAVVGLIFAAGIFT 300 Query: 296 GILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAEAA 355 GIL+GT MVDAM+ SL+++IPD +GP+L +ITA+VSMPFTFFMSNDAFY+GVLP++AEAA Sbjct: 301 GILTGTGMVDAMSKSLLAVIPDFLGPYLAVITALVSMPFTFFMSNDAFYYGVLPVLAEAA 360 Query: 356 SAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTTIVMT 415 S YGI A E+ RAS++GQPVHLLSPLVPSTYLLV +AG+ FGDHQ+FT+KWAV I + Sbjct: 361 SHYGITAVEMARASIVGQPVHLLSPLVPSTYLLVALAGIDFGDHQRFTLKWAVLVCICIL 420 Query: 416 IAALLIG 422 IAALL+G Sbjct: 421 IAALLLG 427 Lambda K H 0.328 0.142 0.411 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: 739 Number of extensions: 28 Number of successful extensions: 2 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: 426 Length of database: 435 Length adjustment: 32 Effective length of query: 394 Effective length of database: 403 Effective search space: 158782 Effective search space used: 158782 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 (21.7 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