Align Fructose import permease protein FrcC (characterized)
to candidate H281DRAFT_03225 H281DRAFT_03225 mannose ABC transporter membrane protein /fructose ABC transporter membrane protein /ribose ABC transporter membrane protein
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Burk376:H281DRAFT_03225 Length = 328 Score = 265 bits (678), Expect = 1e-75 Identities = 141/317 (44%), Positives = 199/317 (62%), Gaps = 9/317 (2%) Query: 40 QHFLHSSPAAV---PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLV 96 +HF P+ PLI LVL+ F + +F S ++LILQQ +V ++ QTL+ Sbjct: 12 RHFSDRLPSLAEVGPLIALVLAC-GFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLI 70 Query: 97 ILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLP 156 +LT GIDLS G +M S+IM +F G PPAL+++CG+G L G +NG L+ R+KLP Sbjct: 71 VLTGGIDLSCGMVMAFGSIIMTKFAVTLGLPPALAILCGIGASTLFGVLNGVLITRIKLP 130 Query: 157 PFIVTLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVL 216 FIVTLG I A +YS A+ +S + FFG F++G A TYG V+ +L Sbjct: 131 AFIVTLGTLNIAFALTQIYS-----NAESVSNLPDAIMFFGNTFKLGPADVTYGTVLTLL 185 Query: 217 LVCLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGR 276 + W+VL T GR++YA+G++ EAA+L G++ ++L+++YTL+G I +A + R Sbjct: 186 MYLATWFVLRDTVPGRHLYALGNNAEAARLMGLSSQKILLTVYTLAGAIYGVAALLSVSR 245 Query: 277 IGSVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQW 336 G P AGQ N++SITAVV+GG SLFGGRGSI G L GALIVGVF GL L+G + Sbjct: 246 TGVGDPQAGQTENLDSITAVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVY 305 Query: 337 TYLLIGLLIIIAVAIDQ 353 L+ G+L+I+AVA D+ Sbjct: 306 QVLITGMLVILAVAADK 322 Lambda K H 0.327 0.141 0.420 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: 362 Number of extensions: 20 Number of successful extensions: 2 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: 360 Length of database: 328 Length adjustment: 29 Effective length of query: 331 Effective length of database: 299 Effective search space: 98969 Effective search space used: 98969 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: 49 (23.5 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