Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate Echvi_0794 Echvi_0794 choline/carnitine/betaine transport
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Cola:Echvi_0794 Length = 529 Score = 467 bits (1201), Expect = e-136 Identities = 237/517 (45%), Positives = 333/517 (64%), Gaps = 22/517 (4%) Query: 40 DIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLV 99 D+H VF + + I++F+ TL + +E F ++ ++ W F+ + N+F++ C Sbjct: 7 DVHAPVFWPASVLIIIFIAITLIVGEPMEKAFDAIKFFITDKTGWLFIIAINIFIVFCFY 66 Query: 100 LIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIE 159 L + G +R+GG +A ++S + W AMLF+AGMGIGL+F+GV+EP+SH++ G Sbjct: 67 LAFSKYGTIRLGGKDAETEFSTSAWFAMLFSAGMGIGLLFWGVAEPVSHYAKPPYGEPFS 126 Query: 160 NGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTM 219 G ++ GM T HW H W+IYA++AL LA F+FN+ LPLT+ Sbjct: 127 IG-----------------SAQRGMNLTFLHWGFHAWAIYAVVALALAFFTFNRKLPLTI 169 Query: 220 RSIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQ 279 RSIFYP+ G+R+ GW+G +ID++AV+AT+FGLATSLG+G Q GLN+LF V ++ T Q Sbjct: 170 RSIFYPILGDRIHGWIGDVIDVMAVLATLFGLATSLGFGVRQINGGLNYLFDVDISVTVQ 229 Query: 280 VVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIAS 339 V+LI IT +A SV +GLD GV+ LSE N+ +AA LL FVI+ GPT+ I GF N+ + Sbjct: 230 VLLISGITLMATASVFSGLDKGVRVLSEWNVRIAAALLIFVILAGPTVFIFRGFVQNLGN 289 Query: 340 YITNIPALSMPFEREDVNYSQG-WTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVI 398 Y+ A+S E N QG WT FYWAWW+SWSPFVGMFIAR+S+GR++REFI+ V+ Sbjct: 290 YLNQFIAVSTWTEAYRDNEWQGTWTIFYWAWWVSWSPFVGMFIARISKGRTIREFILGVL 349 Query: 399 LIPSTVCVLWMTAFGGTAI---SQYVNDGYEAVFNAELPLKLFAMLDVMPFAEITSVVGI 455 L+P+ + W+TA GG+AI Q + + LF L P + + S +G+ Sbjct: 350 LVPALLTFFWLTAMGGSAIFMDMQNETHQFAKDIIKDESTALFVFLHEFPLSTLGSGIGV 409 Query: 456 ILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAM 515 +LV+ FF+TSSDSGSLVID+I AGGK+DAP QR+FW EG VA L++GGGL A Q Sbjct: 410 LLVMSFFVTSSDSGSLVIDSITAGGKLDAPVGQRIFWALAEGTVAAVLLIGGGLTALQTA 469 Query: 516 AVTTGLPFTIVLLVATVSLIKGLMDEPRLSTKAVKKD 552 +TTGLPF IVLL+ SL +GL E +A+K+D Sbjct: 470 TITTGLPFLIVLLIMCFSLFRGLQKE-HARKEALKQD 505 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: 875 Number of extensions: 40 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: 529 Length adjustment: 35 Effective length of query: 518 Effective length of database: 494 Effective search space: 255892 Effective search space used: 255892 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: 52 (24.6 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