Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 157 bits (398), Expect = 3e-43 Identities = 97/306 (31%), Positives = 163/306 (53%), Gaps = 15/306 (4%) Query: 31 IGIFVLC---TLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGS----- 82 IG+ +LC TL+ NF + N+ + + GI A M + + SG DLSVGS Sbjct: 45 IGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAALI 104 Query: 83 ---VIACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQ 139 VI +A V+ +V +G+ A+V+G + GL++G++I K R+ I TL T+ Sbjct: 105 AGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLG 164 Query: 140 IVRGLAYIFANGKAVGVSQESFFVFGN---GQMFGVPVPILITIVCFLFFGWLLNYTTYG 196 I R F+NG A+ + + ++ + GVP+P+ I ++ + G +LN T YG Sbjct: 165 IFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVILNRTAYG 224 Query: 197 RNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELT 256 R AIG N++ A A V+V + KI+ + + GV +A ++ R+ S P G +EL Sbjct: 225 RYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLWELE 284 Query: 257 VISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFY-QYVIRGSILLLAVV 315 I+A ++GG L GG G I + G ++L++I N +NL +I + Y ++G +++ Sbjct: 285 AIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIAVAF 344 Query: 316 IDRLKQ 321 + R K+ Sbjct: 345 MQRGKR 350 Lambda K H 0.330 0.144 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: 253 Number of extensions: 16 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: 322 Length of database: 350 Length adjustment: 28 Effective length of query: 294 Effective length of database: 322 Effective search space: 94668 Effective search space used: 94668 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 (21.8 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