Align Fructose import permease protein FrcC (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 143 bits (360), Expect = 8e-39 Identities = 104/310 (33%), Positives = 162/310 (52%), Gaps = 13/310 (4%) Query: 51 PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVG--A 108 P+I LVL IA G +L F + + +L + A +GI+ VI++ GIDLSVG A Sbjct: 43 PVIGLVLLCIA-GTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMA 101 Query: 109 IMVLSSVI--MGQFTFRYGFPPALSVI---CGLGVGALCGYINGTLVARMKLPPFIVTLG 163 ++ SVI M G P A V+ + +GA+ G ++G L+ + ++ PFIVTLG Sbjct: 102 ALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLG 161 Query: 164 MWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWY 223 I A +S I ++ ++ ++ + V+ + +V +V V Sbjct: 162 TLGIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGV----- 216 Query: 224 VLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPT 283 +LNRTA+GRYV A+G + + A+ A V+V ++ I Y L G+ +A + R+GS SPT Sbjct: 217 ILNRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPT 276 Query: 284 AGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGL 343 G +E+I AV++GG L GG GSI G + GA+++ V S L L + + Sbjct: 277 TGLLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQG 336 Query: 344 LIIIAVAIDQ 353 +IIAVA Q Sbjct: 337 FVIIAVAFMQ 346 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: 359 Number of extensions: 32 Number of successful extensions: 3 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: 350 Length adjustment: 29 Effective length of query: 331 Effective length of database: 321 Effective search space: 106251 Effective search space used: 106251 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