Align Inner-membrane translocator (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 134 bits (337), Expect = 3e-36 Identities = 97/306 (31%), Positives = 161/306 (52%), Gaps = 16/306 (5%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L+ + + GT FA+ V N+L AF+ I A+GM VIISGGIDLSVG++ AL + Sbjct: 47 LVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAAL--I 104 Query: 76 VTSLLITEYQWHPLL----AFVVI-----LPLGTLFGALMGTIIHVYKLQPFIVTLAGMF 126 S+++ P+L A VV+ + LG +FG + G +I +++PFIVTL + Sbjct: 105 AGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLG 164 Query: 127 LARGLATTLSEE-SIAIDHPFYDAVAEMSIA-LPGNGALDLSSLIFILFFVIIAVVMHYT 184 + R T S +I +++ D + + A L G + + IF+L ++ V+++ T Sbjct: 165 IFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLG---VPIPVWIFLLVAIVGGVILNRT 221 Query: 185 RFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGV 244 +G V AIG N+ A+ + + K I Y + +A +++ S + Sbjct: 222 AYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLW 281 Query: 245 ELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFF 304 EL+AIAAV++GGT+L GG+G + GTV+G IL+ VI + +S + V G ++ Sbjct: 282 ELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIA 341 Query: 305 FILLQK 310 +Q+ Sbjct: 342 VAFMQR 347 Lambda K H 0.330 0.145 0.424 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: 353 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: 320 Length of database: 350 Length adjustment: 28 Effective length of query: 292 Effective length of database: 322 Effective search space: 94024 Effective search space used: 94024 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