Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease
Query= uniprot:A3DE71 (289 letters) >NCBI__GCF_003217235.1:WP_110753066.1 Length = 274 Score = 159 bits (403), Expect = 5e-44 Identities = 94/280 (33%), Positives = 160/280 (57%), Gaps = 17/280 (6%) Query: 17 KDTIANIILAILVVLTLGPIVFMV--LTSLMDHNAIARGKW---IAPTRF--SNYVEVFQ 69 K ++ + A+LV + + P +F + SL I G + + P RF SNY ++F Sbjct: 4 KSILSKLGTALLVFVIVSPAIFFFVWMLSLSLKYEIDNGAYPPILIPERFAWSNYTQIFA 63 Query: 70 KLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFL 129 + F +YF NSL+V + ++AL++ AGY +A+ K S ++I+ ++ PG+ +L Sbjct: 64 ENDFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSA---VVIMIARMTPGLSYL 120 Query: 130 LPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDG 189 +PL+L F Q G L+ ++ +I++ VP IWI+ G+F + P ELEEAA+IDG Sbjct: 121 IPLFLLF----QTLG--LLGTLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEAAQIDG 174 Query: 190 CNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYT 249 N + F V LP+A PGIV + I + +W+ +F ++L + T+P + +++ Sbjct: 175 ANAWQVFRLVALPIAKPGIVVSLILAVIFSWNNFVFG-IVLASRETRTLPVAVYNMLSFE 233 Query: 250 TARYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + L AA +VT+PVL++ Q++ ++G+TAGAVKG Sbjct: 234 QVSWGPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273 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: 247 Number of extensions: 13 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: 289 Length of database: 274 Length adjustment: 26 Effective length of query: 263 Effective length of database: 248 Effective search space: 65224 Effective search space used: 65224 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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