Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate PP_0229 PP_0229 choline/carnitine/betaine transporter
Query= SwissProt::Q79VE0 (615 letters) >FitnessBrowser__Putida:PP_0229 Length = 667 Score = 340 bits (873), Expect = 9e-98 Identities = 173/495 (34%), Positives = 278/495 (56%), Gaps = 9/495 (1%) Query: 19 LKSDPFIFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLM 78 ++ +P +F + FI++F + I+ + A A W +GW Y+ ++L +F++ Sbjct: 13 IRMNPPVFYFAASFILIFGLVVISNPQAAGDWLLAAQNWAANTVGWYYMLAMTLYLVFVV 72 Query: 79 GIFASRYGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEE 138 S YG++KLG D D+PE + + W MLFA G+ L F+ V+EP+ H P E Sbjct: 73 VTALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMLQPPQG--E 130 Query: 139 SMSEAAIVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGKHIYS 198 + + A QA F H+G+H W + A G++L YF Y+ LP L S P++GK I Sbjct: 131 AGTVEAGRQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRING 190 Query: 199 TPGKLIDVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIILIITAVACIS 258 G +D I+ T FG+ +G GVL +NAG++ L+ WVQ+++I ++ A Sbjct: 191 PIGYAVDGFGIIATVFGLGADMGFGVLHLNAGLDYLFGISHSQWVQVILITLMMGAAVAV 250 Query: 259 VASGLDKGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDS 318 +G++KG++++S+IN+ +A AL+ F+LF GPT L L+++ G Y +P F + Sbjct: 251 AVAGVEKGVRVMSDINLFLACALLLFVLFAGPTQHLFNTLIQNLGDYLGALPRKSFDVYA 310 Query: 319 FQDNPGWQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSI 378 + +N GW G WTVFYWAW I W+P+VG+F+ARISRGRT+REF+ GVL +P F + W SI Sbjct: 311 YGENRGWLGGWTVFYWAWWIAWAPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSI 370 Query: 379 FGRAGIEVELSNPGFLTQPTVVEGDVPAALFNVLQEYPLTGIVSAFALVIIVIFFITSID 438 FG + ++ ++ N G + +L+ +L+ YP + V A + I +FF+TS D Sbjct: 371 FGNSALD-QVINHGMTALGQSALDNPSMSLYLLLETYPWSKAVIATTVFISFVFFVTSAD 429 Query: 439 SAALV-NDMFATG--AENQTPTSYRVMWACTIGAVAGSLLIISPSSGIATLQEVVIIVAF 495 S +V + + A G A+ P R+ W + +LL + I +L+ V++ + Sbjct: 430 SGTVVLSTLSAKGGDADEDGPNWLRIFWGAMTALITSALLF---AGSIDSLKSAVVLTSL 486 Query: 496 PFFLVQFVMMFSLLK 510 PF L+ MM+ L K Sbjct: 487 PFSLILLCMMWGLHK 501 Lambda K H 0.324 0.140 0.434 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: 1067 Number of extensions: 62 Number of successful extensions: 4 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: 615 Length of database: 667 Length adjustment: 38 Effective length of query: 577 Effective length of database: 629 Effective search space: 362933 Effective search space used: 362933 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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