Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF140 Psest_0140 choline/carnitine/betaine transport
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__psRCH2:GFF140 Length = 685 Score = 416 bits (1068), Expect = e-120 Identities = 205/504 (40%), Positives = 317/504 (62%), Gaps = 26/504 (5%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF + + +L V+ T++ + F+ A++ +N WF++ S F++ + + +TP Sbjct: 16 VFIPAVIVTLLLVIGTISNPELAGEVFSSTLAFITTNFGWFYMLSVAFFLVFIVGIAMTP 75 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G +++G A P YS+ W AMLF+AG GI L+FFGV+EP+ H++S Sbjct: 76 WGSIKLGPDHAEPQYSFPAWFAMLFSAGYGIALLFFGVAEPVLHYAS------------- 122 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P GA G+T A+ M +HW H W+IY L L LA FSF GLPL+MRS Y Sbjct: 123 ---PPAGA-GETVDAAKQAMQIAFFHWGFHIWAIYGLTGLVLAYFSFRHGLPLSMRSALY 178 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLF-GVPMTDTTQVVLI 283 P+ GER+ G +GH++DI A++ T+FG+AT+LG +Q G+N+L+ +P++ Q++ I Sbjct: 179 PIIGERIHGPIGHVVDIFAILGTLFGIATTLGLSVTQINAGINYLWPSIPISINVQIIAI 238 Query: 284 VVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITN 343 +IT LA+ SVVAGLD GVK LS +NM+LA L+ FV +VGP++ IL F N SY+ N Sbjct: 239 AIITGLAICSVVAGLDKGVKNLSLLNMVLAIGLMLFVFLVGPSIFILETFLQNTGSYLNN 298 Query: 344 IPALSM---PFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILI 400 I + + R D + WT F + W I+WSPFVG+FIA++SRGR++R+F+ V+ + Sbjct: 299 IIERTFNLQAYSRSD--WIGNWTLFIFGWTIAWSPFVGLFIAKISRGRTIRQFVFGVMFV 356 Query: 401 PSTVCVLWMTAFGGTAISQYVNDGYEAVFN---AELPLKLFAMLDVMPFAEITSVVGIIL 457 P+ LW + FG TA+ + +GY ++ + A+ + LF + +++P I S + ++L Sbjct: 357 PTIFTFLWFSVFGDTALHMIMVEGYTSLISDVQADNAIALFKLFELLPLTSIASFLAVVL 416 Query: 458 VVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAV 517 ++ FF+TSSDSGSLVID++AAGG + P QRVFW + EG+VA L+L GGL+A Q M + Sbjct: 417 IITFFVTSSDSGSLVIDSLAAGGALHTPVWQRVFWASIEGIVASTLLLAGGLSALQTMTI 476 Query: 518 TTGLPFTIVLLVATVSLIKGLMDE 541 + LPF I++++A + + + L+ E Sbjct: 477 ASALPFAIIMMIAALGMWRALVIE 500 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: 958 Number of extensions: 56 Number of successful extensions: 5 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: 685 Length adjustment: 37 Effective length of query: 516 Effective length of database: 648 Effective search space: 334368 Effective search space used: 334368 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