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:D8IZC8 (344 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 184 bits (466), Expect = 4e-51 Identities = 129/343 (37%), Positives = 183/343 (53%), Gaps = 20/343 (5%) Query: 4 TKMTHTHDAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASA 63 T + DA P RRS T L LG+ L+ + +LF L+ + GT F++ Sbjct: 3 TTPLNNQDAAP--VRRSG--TYFGLGTYLGLAGALLAMIVLFSFLSSHFWSYGT--FSTL 56 Query: 64 ENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMF 123 N Q+ +VLA GMTFV++ GIDLSVGSVLA++A LG GW + Sbjct: 57 AN------QIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGW--GWGVLPS 108 Query: 124 IFSGLVM----GMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEW 179 G+ + G + G + I +F+V+LG + RG AY D T D ++ W Sbjct: 109 ALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAYQFTDSRTAYIGD--AYAW 166 Query: 180 IGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFV 239 N V +A+ V++L+ ++L +TV G ++ IG N +A RL GI + V Sbjct: 167 FSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTNEEAVRLAGIDPRPYKVLV 226 Query: 240 YSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGAL 299 +++ GL +GLA SRL A+ N GSG EL IAAVV+GGTSLMGG GS+ T G L Sbjct: 227 FALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 286 Query: 300 IIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAAQ 342 II V+ GL +G S + + GAVIV+AV+LD +R + A + Sbjct: 287 IISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYRSRRAGR 329 Lambda K H 0.324 0.138 0.417 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: 305 Number of extensions: 13 Number of successful extensions: 4 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: 344 Length of database: 331 Length adjustment: 28 Effective length of query: 316 Effective length of database: 303 Effective search space: 95748 Effective search space used: 95748 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: 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