Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 197 bits (502), Expect = 2e-55 Identities = 111/304 (36%), Positives = 169/304 (55%), Gaps = 9/304 (2%) Query: 42 SLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCA 101 +LL MI+ FSF S +F ++ VLA+ T+V+I GIDLSVG+++ A Sbjct: 32 ALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAA 91 Query: 102 VMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLV 161 V + WG + + AL+G I+G V ++P FI +LG++ + +GL+ Sbjct: 92 STVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAYQ 151 Query: 162 ISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYT 221 + +R Y D ++ + G + A +I LV + A ++L +TVFGRY Sbjct: 152 FTDSRTAYIGDA--YAWFSNPVAFG-------VSPAFIIALLVIVLAQLVLTRTVFGRYL 202 Query: 222 FALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIA 281 +G+NEEA+RL+G+ +KV V+ G + G+A L SRL +A P G G EL IA Sbjct: 203 IGIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIA 262 Query: 282 AVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDIL 341 AVVIGGTSL GG G+++ T G I+SVL GL + ++ + ++TG +I++AV LD Sbjct: 263 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTY 322 Query: 342 RRRR 345 R RR Sbjct: 323 RSRR 326 Lambda K H 0.326 0.139 0.398 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: 260 Number of extensions: 17 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: 347 Length of database: 331 Length adjustment: 28 Effective length of query: 319 Effective length of database: 303 Effective search space: 96657 Effective search space used: 96657 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