Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_086508159.1 BZY95_RS01105 maltose ABC transporter permease MalG
Query= uniprot:A3DE71 (289 letters) >NCBI__GCF_002151265.1:WP_086508159.1 Length = 296 Score = 122 bits (306), Expect = 1e-32 Identities = 88/293 (30%), Positives = 146/293 (49%), Gaps = 18/293 (6%) Query: 12 RKKKIKDTIANIILAILVVLTLGPIVFMVLTSLMDHNAIARGKWIAPTRFS--------- 62 R + + A++ L + L L P++ ++ S + N A G I P RFS Sbjct: 7 RSLRWRKLAAHLALIGFLTLILFPLLLVISISFREGN-FATGSLI-PERFSLEHWSLALG 64 Query: 63 ------NYVEVFQKLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGIL 116 + V P ++ NS+ V + ++ ++++T + Y+ A+ +F G G Sbjct: 65 IPWERADGTVVQPPFPVLLWLWNSVKVAIVSSLLIVLLSTTSAYAFARMRFAGKGPILKS 124 Query: 117 ILATQLLPGMMFLLPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFAS 176 +L Q+ P ++ L+ LY F ++ Q G IN+ G +IV S V IW I+G+F S Sbjct: 125 MLIFQMFPAVLSLVALYALFDRLGQFVGWLGINT-HGALIVASLGAVALHIWTIKGYFES 183 Query: 177 IPGELEEAARIDGCNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVT 236 I G LEEAA +DG + + AF ++LPL++P ++ I F+ + E A VLL D Sbjct: 184 IDGSLEEAAMVDGASTWQAFRYILLPLSLPILMVVFILAFVMSIMEYPMASVLLVDEHKL 243 Query: 237 TIPAGIRGFIAYTTARYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 T+ G + ++A R+ AA + +P+ + F Q+ I G+TAG VKG Sbjct: 244 TLAVGAQQYLADHNQRWGNFAAAAVLSGLPITLAFLICQRWIIGGLTAGGVKG 296 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: 205 Number of extensions: 5 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: 289 Length of database: 296 Length adjustment: 26 Effective length of query: 263 Effective length of database: 270 Effective search space: 71010 Effective search space used: 71010 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 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