Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate Pf6N2E2_1038 citrate transporter
Query= TCDB::P42308 (426 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1038 Length = 428 Score = 438 bits (1126), Expect = e-127 Identities = 218/434 (50%), Positives = 307/434 (70%), Gaps = 18/434 (4%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 ML L + M+ FMYLIMS RLS L+AL++VPIVF +SGF LG MM G+ LAPTG Sbjct: 1 MLIFLSYAMIASFMYLIMSKRLSPLVALLLVPIVFGCLSGFTTQLGGMMYDGIKMLAPTG 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 IML FAILYF +M D+GLF+PLI +L VKGDP KI +GTAVL + + LDGDG TTY+I Sbjct: 61 IMLTFAILYFCMMTDAGLFNPLIKVLLRLVKGDPRKIVIGTAVLGLCVGLDGDGATTYII 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180 AA LP+Y+ G+ V+A + ++ GVMNI+PW GP +R +++ +D +E+F ++P Sbjct: 121 ATAAFLPIYRLTGIRLQVMATVLLMAIGVMNILPWAGPFSRAASAMHVDITELFLEMVPV 180 Query: 181 MIAGILWVIAVAYILGKKERKRLGVISID---------HAPSSDPEAAPLKRPALQWFNL 231 MIAG +WVI A+ LG+ E +RLG+I++ H SDP+ N+ Sbjct: 181 MIAGGVWVIFAAWWLGRMEYRRLGLIAVSEDEVLKGYAHIRLSDPKFL---------LNV 231 Query: 232 LLTVALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAA 291 +LTVAL++ ++ +L+PLP+LFM AF +A +VN+P +K+Q++ I+ HA N + V ++FAA Sbjct: 232 VLTVALISCMMLNLMPLPILFMVAFGLACLVNFPTLKQQKEVIARHADNVMAVTLLIFAA 291 Query: 292 GIFTGILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPII 351 GIF GI+ GT M+ A++ +L++L+P G ++ +ITA++SMPFT+ ++NDAFYFGVLPI+ Sbjct: 292 GIFVGIMGGTGMIKAISDNLITLLPQQAGHYMSVITALLSMPFTYVLTNDAFYFGVLPIL 351 Query: 352 AEAASAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTT 411 AE A+ YGI E+ ASL+GQPVHLLSPLV STYLL G+ + +GD+Q+ ++KW GT Sbjct: 352 AETAAHYGIGPNEMAIASLIGQPVHLLSPLVASTYLLCGLLDIDYGDNQRVSLKWTFGTV 411 Query: 412 IVMTIAALLIGIIS 425 IVM AA+ IG I+ Sbjct: 412 IVMLFAAIAIGAIT 425 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: 640 Number of extensions: 37 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: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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