Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate PP_3957 PP_3957 choline/carnitine/betaine transporter BetTC
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Putida:PP_3957 Length = 657 Score = 446 bits (1146), Expect = e-129 Identities = 219/500 (43%), Positives = 323/500 (64%), Gaps = 25/500 (5%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF S + + L V+ F++ + F ++ W+++N WF++ + +I + L V+ Sbjct: 15 VFYTSAILVFLLVLYATAFQEHAQTLFEQVQRWIITNASWFYILVVALVLISVVFLAVSR 74 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G +++G + PDY + W AMLF+AGMGIGL+FFGV+EP+ HFS+ Sbjct: 75 YGDIKLGPDHSEPDYRKSSWFAMLFSAGMGIGLMFFGVAEPVMHFSTP------------ 122 Query: 165 DWAPLGGAVGD--TDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSI 222 VGD T AA+ M T +HW LH W+IYA++AL LA FSF GLPLT+RS Sbjct: 123 -------PVGDPGTVAAAREAMKITFFHWGLHAWAIYAIVALILAYFSFRNGLPLTLRSA 175 Query: 223 FYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVL 282 YPL GER++G +GH +D+ A++ TVFG+ATSLGYG Q +G + +FG+P+ T QV+L Sbjct: 176 LYPLIGERIYGPIGHAVDVFAILGTVFGVATSLGYGVLQINSGFHHVFGLPVNTTVQVIL 235 Query: 283 IVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYIT 342 I ALA +SV +GLD G++ LSE+N+ LA +L+ FV+++GPT+ +L + N +Y++ Sbjct: 236 ITATCALATLSVASGLDKGIRILSELNLSLAVILMLFVLLLGPTVFLLQTYVQNTGAYLS 295 Query: 343 NIPALSMP-FEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIP 401 +I + + E ++ GWT YW WW+SWSPFVG+FIAR+SRGR++REF+ V+ +P Sbjct: 296 DIVNKTFNLYAYEPTDWIGGWTLLYWGWWLSWSPFVGLFIARISRGRTIREFVCGVLFVP 355 Query: 402 STVCVLWMTAFGGTAISQYVNDGYE---AVFNAELPLKLFAMLDVMPFAEITSVVGIILV 458 + +LWMT FG +AI +NDG + AV + + L LFA L+ PF+ I S+V +++V Sbjct: 356 AGFTLLWMTVFGDSAIHMILNDGVKDLAAVVSEDSSLALFAFLEHFPFSSIISLVAVLMV 415 Query: 459 VVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAVT 518 VVFF+TS+DSG+LV+D +A+ G+ +P QR+FW G VAIAL+L GL A Q + Sbjct: 416 VVFFVTSADSGALVVDMLASSGQGHSPLWQRIFWSVCIGAVAIALLLANGLKALQTATIA 475 Query: 519 TGLPFTIVLLVATVSLIKGL 538 + LPF ++LLVA L K L Sbjct: 476 SALPFAVILLVAIWGLFKAL 495 Lambda K H 0.327 0.141 0.435 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: 942 Number of extensions: 42 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: 553 Length of database: 657 Length adjustment: 37 Effective length of query: 516 Effective length of database: 620 Effective search space: 319920 Effective search space used: 319920 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: 53 (25.0 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