Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate H281DRAFT_03810 H281DRAFT_03810 citrate-Mg2+:H+ or citrate-Ca2+:H+ symporter, CitMHS family
Query= TCDB::P42308 (426 letters) >FitnessBrowser__Burk376:H281DRAFT_03810 Length = 434 Score = 371 bits (952), Expect = e-107 Identities = 194/434 (44%), Positives = 275/434 (63%), Gaps = 10/434 (2%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 ML +LG ++V + I+S R+S L+ALI+VPI +LI GFG + +I G+ LAP Sbjct: 1 MLPLLGLATIVVLLGAILSKRMSPLVALIIVPIAASLIGGFGFQTSKFVIDGLKGLAPVV 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 M +FAILYFG + D+G DP+I +IL V P +I +GT +L + I LDG G +++ Sbjct: 61 GMFVFAILYFGTITDAGTLDPIIDRILRAVGTRPTRIVMGTTLLALLIHLDGSGAVCFLV 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180 TI AMLPLY RL M+R VLA + +G+ N +PW GP R ASL L S +F PLIP Sbjct: 121 TIPAMLPLYDRLKMDRRVLAAAVSMAAGI-NFLPWTGPMIRASASLHLPISALFNPLIPV 179 Query: 181 MIAGILWVIAVAYILGKKERKRLGVISIDHA---PSSD--PEAAPLKRPALQWFNLLLTV 235 G+++V VA+ LG++E KRLG + A P + PE L+RP WFN++LT+ Sbjct: 180 QAIGLVFVFGVAFWLGRREEKRLGFGAASGAVPMPKRELTPEEQALRRPKNFWFNIVLTI 239 Query: 236 ALMAALIT--SLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGI 293 ++ ++ +P ++FM VALMVNYPNV Q+KRI AHA AL + ++ AAG+ Sbjct: 240 VVLGTMVVMGEKIPPAIMFMVGLCVALMVNYPNVDMQRKRIDAHARAALMMAGILLAAGV 299 Query: 294 FTGILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAE 353 FTG++ G+ M+ AMA + V +P AM H+P+ I+SMP + D+FYFGVLP+IAE Sbjct: 300 FTGVMQGSGMLKAMAQAAVGFVPPAMASHIPVALGIMSMPLSMLFDPDSFYFGVLPVIAE 359 Query: 354 AASAYGIDAAEIGRASLLGQPV--HLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTT 411 A G+ A ++G+A+LLGQ +SPL P+T+L+VG+ G+ DHQ+FT G + Sbjct: 360 VAGQLGVPAVQVGQAALLGQMTTGFPVSPLTPATFLVVGLCGIELADHQRFTFPLLFGAS 419 Query: 412 IVMTIAALLIGIIS 425 IVMTIA + +GI S Sbjct: 420 IVMTIACVALGIFS 433 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: 675 Number of extensions: 41 Number of successful extensions: 6 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: 434 Length adjustment: 32 Effective length of query: 394 Effective length of database: 402 Effective search space: 158388 Effective search space used: 158388 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