Align ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 401 bits (1030), Expect = e-116 Identities = 203/305 (66%), Positives = 254/305 (83%) Query: 17 LGTYLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLS 76 LGTYLGL L MVALFS LS +F S +TF T+AN+IP L V+AVGMTFVLII GIDLS Sbjct: 586 LGTYLGLLAVLAGMVALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLS 645 Query: 77 VGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVL 136 VGSV+ALAA+ + AIL WGW+V AA L +A + GTITG+I+VAWR+PSFIVSLG+L Sbjct: 646 VGSVMALAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGML 705 Query: 137 EMARGLAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYL 196 E RG AY +T SRT Y+GDA +WLS P GIS +F++A++++ +AQ VL+RTVFGR + Sbjct: 706 EAVRGSAYVVTDSRTQYVGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCV 765 Query: 197 IGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIA 256 +GIGTNEEA+RLAG++P+P +++VF++ GLLAG+A L Q +RLEAADPNAG+G+ELQVIA Sbjct: 766 VGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIA 825 Query: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316 AVVIGGTSLMGGRGSV++T FGVLII+VL AGLAQ+GA+EP+KRIITG VIV AV++DT Sbjct: 826 AVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTL 885 Query: 317 RSQRA 321 R +RA Sbjct: 886 RQRRA 890 Lambda K H 0.325 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: 617 Number of extensions: 19 Number of successful extensions: 1 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: 325 Length of database: 892 Length adjustment: 35 Effective length of query: 290 Effective length of database: 857 Effective search space: 248530 Effective search space used: 248530 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: 52 (24.6 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