Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 203 bits (516), Expect = 2e-56 Identities = 129/336 (38%), Positives = 190/336 (56%), Gaps = 16/336 (4%) Query: 9 THDAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMN 68 T A P S+S L LG+L VL + LF L+ Y F SAE + Sbjct: 567 TAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMVALFSSLSEY--------FWSAETFIT 618 Query: 69 ILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIP----MFI 124 I ++ V+A GMTFV++ AGIDLSVGSV+A++A L GW +P + + Sbjct: 619 IANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQW--GWTVPAAAALAL 676 Query: 125 FSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGD 184 +GLV G + GA+ + +F+V+LG + A RG+AY++ D T D + W+ Sbjct: 677 ATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQYVGD--AISWLSAPF 734 Query: 185 FLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISG 244 F + + +AV +V+++ ++L +TV G + IG N +A RL G+ + + V++++G Sbjct: 735 FGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTG 794 Query: 245 LFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVM 304 L +GLAG M ++RL A+ N G+G EL IAAVV+GGTSLMGG GS+ T G LII V+ Sbjct: 795 LLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVL 854 Query: 305 NNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDA 340 GL +G S + + G VIV AVI+D RQ+ A Sbjct: 855 EAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRRA 890 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: 627 Number of extensions: 32 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: 892 Length adjustment: 36 Effective length of query: 308 Effective length of database: 856 Effective search space: 263648 Effective search space used: 263648 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: 53 (25.0 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