Align L-lysine transport protein (characterized)
to candidate GFF4360 PS417_22325 amino acid APC transporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__WCS417:GFF4360 Length = 475 Score = 427 bits (1099), Expect = e-124 Identities = 216/478 (45%), Positives = 315/478 (65%), Gaps = 16/478 (3%) Query: 25 LIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRKPHLDS 84 L+AL++GS +G GIFS+PQN+ + A GA+LIGW+I VGML++AFVF LA RKP LD Sbjct: 13 LVALVVGSMIGGGIFSLPQNMAASADVGAVLIGWVITAVGMLTLAFVFQTLANRKPDLDG 72 Query: 85 GVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSALAV 144 GVYAYA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++ P+F + + + + Sbjct: 73 GVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPIFGEGNTPAAVIGA 132 Query: 145 SALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWA-RDG 203 S L W V +V RGI +AAF+ VTTVAK++PL+ F +L+A F + FT D+W ++ Sbjct: 133 SVLLWAVHFLVLRGIKEAAFINLVTTVAKVVPLVLF-VLIALFAFKLDIFTADIWGLKNP 191 Query: 204 GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSISSL 263 +GS+ +QVR +M+ TVWVFIGIEGAS++S +A RSDV +ATVIGF+ VLL L+ ++ L Sbjct: 192 DLGSVMNQVRNMMLVTVWVFIGIEGASIFSARAEKRSDVGKATVIGFITVLLFLMLVNVL 251 Query: 264 SFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPLALM 323 S G++TQ ELA L + SMA+VLE VVG WGA LIS+GL +S+LGA +SW +LCAE + Sbjct: 252 SLGIMTQPELAKLQNPSMAAVLEHVVGHWGAVLISVGLVISLLGALLSWVLLCAEIMFAA 311 Query: 324 AMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLYLVPYL 383 A D +P + N+ A ++ ++QIF++I + +TY+S++ LAT++ LVPYL Sbjct: 312 AKDHTMPEFLRKENANHVPANALWLTNAMVQIFLVITLFSASTYLSLIYLATSMILVPYL 371 Query: 384 FSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYAAEP 443 +SA Y ++LA RG+ E + +E +K L +G +A +Y+VWL YA Sbjct: 372 WSAAYALLLAVRGETY--------------ENALKERQKDLFIGAIALIYAVWLLYAGGT 417 Query: 444 QFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLSL 501 +++L A+ PG I + + G+ +F E + +++ A GL +G L+L Sbjct: 418 KYLLLSALLYAPGAILFAKAKRELGKPIFTNVEKLIFAAVIIGALVAAYGLYDGFLTL 475 Lambda K H 0.327 0.139 0.421 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: 723 Number of extensions: 36 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: 501 Length of database: 475 Length adjustment: 34 Effective length of query: 467 Effective length of database: 441 Effective search space: 205947 Effective search space used: 205947 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