Align Ribose import permease protein RbsC (characterized)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 213 bits (541), Expect = 7e-60 Identities = 116/320 (36%), Positives = 186/320 (58%), Gaps = 8/320 (2%) Query: 2 TTQTVSGRRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAV 61 TT+ R F W+M L+A + + + L NF + N+ + S I A Sbjct: 11 TTRKPLDLRRFLDDWVM----LLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAAC 66 Query: 62 GMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAK 121 M + + DLSVGS++A G VAA ++ + + V AAL +G +G + G+++AK Sbjct: 67 TMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLINGIVIAK 126 Query: 122 GRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGI 181 RV A I TL M ++RG+ ++ NG V + + F FG G+ GVP P+ I + Sbjct: 127 LRVNALITTLATMQIVRGLAYIFANGKAVGV----SQESFFVFGNGQMFGVPVPILITIV 182 Query: 182 VFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVAR 241 FL ++L++T GR A+GGN+ A L+G+NV++ KII++++ G++ +LAG+I +R Sbjct: 183 CFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASR 242 Query: 242 LSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYY 301 ++S QP G G+EL I+A VLGG SL+GG G I + G LIL + N +NL + ++Y Sbjct: 243 MTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFY 302 Query: 302 QMIVKAVVILLAVLVDNKKQ 321 Q +++ ++LLAV++D KQ Sbjct: 303 QYVIRGSILLLAVVIDRLKQ 322 Lambda K H 0.324 0.139 0.393 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: 238 Number of extensions: 10 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: 321 Length of database: 323 Length adjustment: 28 Effective length of query: 293 Effective length of database: 295 Effective search space: 86435 Effective search space used: 86435 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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