Align Sucrose permease; Sucrose transport protein (characterized)
to candidate 14481 b0343 galactoside permease (NCBI)
Query= SwissProt::P30000 (415 letters) >FitnessBrowser__Keio:14481 Length = 417 Score = 231 bits (590), Expect = 2e-65 Identities = 123/397 (30%), Positives = 216/397 (54%), Gaps = 12/397 (3%) Query: 11 YYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQ 70 ++ F + F FFI + ++ + IWL ++ ++ G +++ S+LF +G++ Sbjct: 9 FWMFGLFFFFYFFIMGA-YFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLS 67 Query: 71 DKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDS 130 DKLGL+K L+W ++ +LV+ PF I+++ PLLQ N VG I+G ++ G + AG +++ Sbjct: 68 DKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEA 127 Query: 131 FTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRF 190 F EK++R +FE+G AR +G G+A+ A GI F+I+ FWL S G ++ + F Sbjct: 128 FIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGS--GCALILAVLLF 185 Query: 191 ---KDKDHQCIAADAGGVKKEDF-----IAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFP 242 D A+A G F + +F+ W ++++G Y++FDQQ F Sbjct: 186 FAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQ-FA 244 Query: 243 VFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRIL 302 F+ F + + GTR++GY+ + +L A M P +NR+G KNALL+ IM++RI+ Sbjct: 245 NFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRII 304 Query: 303 SCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVL 362 + + + ++K LH EVP ++ FKY + F+ R S+TI+L+ F L ++ Sbjct: 305 GSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIF 364 Query: 363 LSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLS 399 +S G +++ G+Q + + + L +F LS Sbjct: 365 MSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLS 401 Score = 27.3 bits (59), Expect = 9e-04 Identities = 41/191 (21%), Positives = 79/191 (41%), Gaps = 12/191 (6%) Query: 215 KDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCM 274 K+ NFW+F +F + FY FP F L + + + G + + + L Sbjct: 5 KNTNFWMFGLF----FFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQ 60 Query: 275 AIIPFFVNRVGPKNALLIGVVIMALRILSCALFV-NPWI---ISLVKLLHAIEVPLCVIS 330 + +++G + LL + M + +F+ P + I + ++ I + C + Sbjct: 61 PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA 120 Query: 331 VFKYSVANFDKRLSSTIFLIG-FQIASSLGIVLLSTPTGILFDHAGYQTVFFAISGIVCL 389 A +K + F G ++ +G L ++ GI+F Q VF+ SG C Sbjct: 121 GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT-INNQFVFWLGSG--CA 177 Query: 390 MLLFGIFFLSK 400 ++L + F +K Sbjct: 178 LILAVLLFFAK 188 Lambda K H 0.333 0.147 0.471 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: 550 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 415 Length of database: 417 Length adjustment: 31 Effective length of query: 384 Effective length of database: 386 Effective search space: 148224 Effective search space used: 148224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.5 bits) S2: 50 (23.9 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