Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate 6937001 Sama_1175 choline/carnitine/betaine transport (RefSeq)
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__SB2B:6937001 Length = 658 Score = 427 bits (1099), Expect = e-124 Identities = 217/508 (42%), Positives = 313/508 (61%), Gaps = 24/508 (4%) Query: 41 IHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVL 100 I+ VF S I L V + QQ + +F ++ WL W ++ VF++ + + Sbjct: 7 INRPVFFGSLFLITLLVALGAIWPQQAQQWFGAVQHWLEVKAGWLYVLGVAVFLVFIVFV 66 Query: 101 IVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIEN 160 +V+ G +++G A PDYSY W+AMLF+AGMGIGL+FFGV+EP+ H + Sbjct: 67 MVSRFGDIKLGPDHAEPDYSYKSWIAMLFSAGMGIGLMFFGVAEPVMHLIAP-------- 118 Query: 161 GVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMR 220 A ++ A+ M T +HW +H W+IYA++AL LA F++ LPL R Sbjct: 119 ---------PDATPESIEAARQAMKITFFHWGIHAWAIYAVVALSLAYFAYRHKLPLLPR 169 Query: 221 SIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFG--VPMTDTT 278 S YPL GER+ G +GH +D AV+ T+FG+ATSLG+G Q GLNFLFG P++ Sbjct: 170 SALYPLIGERIHGPIGHAVDAFAVLGTMFGVATSLGFGVLQVNAGLNFLFGDQFPVSTPL 229 Query: 279 QVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIA 338 QV LI VIT +A +SV +GLD GVKRLSE+N++LA +L+ V++VGPT+A+L N Sbjct: 230 QVGLIAVITLIATVSVFSGLDKGVKRLSELNLLLAVVLMLVVLLVGPTVALLQAIVQNTG 289 Query: 339 SYITNI--PALSMPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIIC 396 +Y ++I ++ ++ ++ GWT YW WWISWSPFVG FIARVSRGR++REF++ Sbjct: 290 AYFSDIVGKTFNLYAYQQKNDWLGGWTLLYWGWWISWSPFVGTFIARVSRGRTIREFLLG 349 Query: 397 VILIPSTVCVLWMTAFGGTAISQYVNDGYEAVFNA---ELPLKLFAMLDVMPFAEITSVV 453 V+ +PS LWMT FG +AI Q ++ G + +A ++ + LF +P + S V Sbjct: 350 VLFVPSGFTFLWMTVFGNSAIDQILHQGNTVLADAVSSDVSVALFVFFQQLPLTSLLSAV 409 Query: 454 GIILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQ 513 + LVV FF+TSSDSGSLVID + +GG + +P QRVFW +G+VA L+L GGL A Q Sbjct: 410 ALCLVVTFFVTSSDSGSLVIDNLTSGGDMSSPVWQRVFWALMQGVVASVLLLAGGLQALQ 469 Query: 514 AMAVTTGLPFTIVLLVATVSLIKGLMDE 541 A+ + +PF +V+L+ + L K L D+ Sbjct: 470 TAAIASAMPFLLVMLLICLGLFKALQDD 497 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: 925 Number of extensions: 54 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: 553 Length of database: 658 Length adjustment: 37 Effective length of query: 516 Effective length of database: 621 Effective search space: 320436 Effective search space used: 320436 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