Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate PP_0147 PP_0147 Citrate transporter
Query= TCDB::P42308 (426 letters) >FitnessBrowser__Putida:PP_0147 Length = 435 Score = 548 bits (1413), Expect = e-161 Identities = 267/428 (62%), Positives = 344/428 (80%), Gaps = 5/428 (1%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 ML LGF M+I FMYLIM+ RLSALIALI+VPI+FAL GF +G MM++G++ LAPTG Sbjct: 1 MLTFLGFAMVITFMYLIMTKRLSALIALILVPILFALFGGFSAKIGPMMLEGISKLAPTG 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +ML+FAILYF +MIDSGLFDP + KIL VKGDPLK++VGTAVL + +SLDGDG TTYMI Sbjct: 61 VMLMFAILYFALMIDSGLFDPAVRKILKLVKGDPLKVSVGTAVLALVVSLDGDGATTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180 AAMLP+Y RLGM+ ++AG+ +L GVMN+ PWGGPTAR ++L +D S++F P+IPA Sbjct: 121 CCAAMLPMYSRLGMSPRIMAGLIILAGGVMNMTPWGGPTARAASALHVDPSDIFVPMIPA 180 Query: 181 MIAGILWVIAVAYILGKKERKRLGVI-----SIDHAPSSDPEAAPLKRPALQWFNLLLTV 235 M+ G+L ++A+AY+ GK+ER RLG + IDH+ + + +RP L +FN LT Sbjct: 181 MLFGVLAILAIAYMYGKRERARLGELHLPTDDIDHSEITVSQYPDARRPKLLYFNGALTA 240 Query: 236 ALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIFT 295 ALM ALI LLPLPVLFM AF++A++VNYP +++Q+ RI+AHAG+ L V ++FAAGIFT Sbjct: 241 ALMVALIAGLLPLPVLFMIAFSIAMIVNYPCLQQQKDRIAAHAGSVLAVTGLIFAAGIFT 300 Query: 296 GILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAEAA 355 GILSGT MVDAM+ SL+++IP+A+GP+L +ITAIVSMPFTFFMSNDAFY+GVLP++AEAA Sbjct: 301 GILSGTGMVDAMSKSLLAVIPEALGPYLAVITAIVSMPFTFFMSNDAFYYGVLPVLAEAA 360 Query: 356 SAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTTIVMT 415 S YGI E+ RAS++GQPVHLLSPLVPSTYLLV +AG+ FGDHQ+FT+KWAV + + Sbjct: 361 SHYGITPVEMARASIVGQPVHLLSPLVPSTYLLVALAGIEFGDHQRFTLKWAVLVCLCIM 420 Query: 416 IAALLIGI 423 + ALL+GI Sbjct: 421 LGALLMGI 428 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: 751 Number of extensions: 32 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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