Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate PP_5061 PP_5061 Choline transporter
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Putida:PP_5061 Length = 667 Score = 469 bits (1208), Expect = e-136 Identities = 247/653 (37%), Positives = 376/653 (57%), Gaps = 20/653 (3%) Query: 49 QRFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFS 108 +R +VN VF S +I + + + P+ A + Q + FGW Y+L + +L Sbjct: 12 ERVRVNRVVFFTSALMILVLTALLIAVPETAGQVLGVAQKWLTRTFGWYYMLVICGYLLF 71 Query: 109 MLFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAE 168 +++LAFS YG LKLG D +P+F Y +W MLF++G+GI L+YF EP+ H+ +PPE Sbjct: 72 VVYLAFSDYGSLKLGGKDDQPDFSYGAWAGMLFSSGIGISLLYFGASEPLDHYFNPPEGT 131 Query: 169 PLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKE-GIH 227 P ++ A R+ + +TF HWG+H WAIY++VGL++ YF YR+N PL +RS LYPL+ E + Sbjct: 132 PASLEAARQGLQLTFLHWGLHGWAIYALVGLAVGYFAYRHNQPLALRSALYPLVGERWVK 191 Query: 228 GPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATI 287 G G+ VDIF + T+ GL T+LG G +Q++SGL YL G+ S L+++ V+ +AT+ Sbjct: 192 GAAGNAVDIFGMFVTLLGLVTNLGIGAMQVSSGLEYLFGMDHSKTNLLVVILVMAGVATV 251 Query: 288 SVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIY 347 + V+GVE G+R LS N+ L L++FVL+ G T L+ FVQN+G YL+ +VL+TF++Y Sbjct: 252 AAVSGVENGIRRLSNLNIMLFSGLLIFVLLGGETLHLLNGFVQNVGDYLNGIVLKTFDLY 311 Query: 348 AYE-----PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTF 402 YE W+ WT+FYWAWWISW PFVGMFIARIS+GRTVR+ V VL +P FT Sbjct: 312 VYEGEAGKSERWLGLWTVFYWAWWISWGPFVGMFIARISKGRTVRQLVMGVLLIPLGFTL 371 Query: 403 LWMTVFGNTAIYVDTTIANG--ELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIF 460 W+++FGNTA+ D I G EL + S++++Q E+ P + +AV + + Sbjct: 372 AWLSIFGNTAL--DLVINQGAVELGKTALEQPSMSIYQLLEHFPAAKIVIGVAVFVGFVL 429 Query: 461 FVTSSDSGSLVIDTIASGG---ETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATIS 517 F+T +DSG++++ ++ G + P +FW + +V LL G A+Q+ + Sbjct: 430 FLTPADSGAVMMANLSCTGGKVDEDAPHWMVVFWSVVITLVTIGLLFAGNFEAMQTMVVL 489 Query: 518 TALPFSLVMLILVWSLFVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRA 577 LPFS+V+++ ++ L+ M+ D+ Q L R + RL P + Sbjct: 490 AGLPFSVVLVLFMFGLYKAMKQDVVIEQERAELAARGRRG----FSERLTQLELQPTQAV 545 Query: 578 VEKFLQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHK 637 V++F+ V PAL+ A +L + + L V E FVY V + + Sbjct: 546 VQRFMDKQVSPALKEAAAQLQTQGFEVETRVGQSRNLMGLRVMMEEGNPFVYEVSLDGYM 605 Query: 638 LPAFTAYDATVADVR---YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERY 687 A ++R Y A + DGS+ YD+MG A +QI+ DVL QFE + Sbjct: 606 AAPSEAPVEGEPELRQRFYRAEVYLHDGSQEYDLMGFAPDQIVRDVLDQFESH 658 Lambda K H 0.326 0.139 0.422 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: 1193 Number of extensions: 65 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: 706 Length of database: 667 Length adjustment: 39 Effective length of query: 667 Effective length of database: 628 Effective search space: 418876 Effective search space used: 418876 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: 54 (25.4 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