Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate RR42_RS22885 RR42_RS22885 sugar ABC transporter permease
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__Cup4G11:RR42_RS22885 Length = 288 Score = 136 bits (343), Expect = 5e-37 Identities = 83/271 (30%), Positives = 144/271 (53%), Gaps = 12/271 (4%) Query: 24 ILAILVVLTLGPIVFMVLTSLMD-HNAIARGK----WIAPTRFSNYVEVFQKLPFGIYFR 78 ILA+ P +M++T+ D H+ I + P N +F + + + Sbjct: 24 ILAVFAGFCAFPFYWMLITTFKDVHDLINTANNPFLFNQPPTLDNLRVLFLETQYLRWIA 83 Query: 79 NSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVK 138 N+L+V ++V+ + L++A AGYSLA+ I I T L+P + +P F + Sbjct: 84 NTLLVGAMVVAITLLLAVPAGYSLARLAGSRGRQLAIAIFLTYLIPPTILFIP----FSR 139 Query: 139 IKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLR 198 I A G+Q +S+ LV+VY +F VPF W++ GFF ++P ++EEAA +DG ++F AFL+ Sbjct: 140 IIGALGLQ--DSLWSLVLVYPSFTVPFCTWLMMGFFKAVPRDIEEAAMMDGLSRFGAFLK 197 Query: 199 VMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARY-DLLM 257 V++PL+ GI+ I+ E ++A + + T+ G+ F+ + LM Sbjct: 198 VVVPLSSAGILTVVIFTLTLVMQEFVYALTFITSSSQYTVSVGVPTFLVRGDVYFWGSLM 257 Query: 258 AAGTIVTIPVLIMFFTMQKKFISGMTAGAVK 288 A +V++PV +++ +F++G T GAVK Sbjct: 258 GACLVVSVPVAVLYNLFVDRFVAGFTVGAVK 288 Lambda K H 0.332 0.145 0.434 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: 231 Number of extensions: 11 Number of successful extensions: 3 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: 289 Length of database: 288 Length adjustment: 26 Effective length of query: 263 Effective length of database: 262 Effective search space: 68906 Effective search space used: 68906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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