Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b21105 SM_b21105 sugar ABC transporter permease
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__Smeli:SM_b21105 Length = 288 Score = 160 bits (406), Expect = 2e-44 Identities = 100/278 (35%), Positives = 152/278 (54%), Gaps = 16/278 (5%) Query: 20 IANIILAILVVLTLGPIVFMVLTSLMDHNAIARGK--WIAPT-RFSNYVEVFQK-----L 71 +A + LA+LV+ G +++VL+SL I WI T Y +F + Sbjct: 19 LAGLFLAMLVICLPG--LWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGV 76 Query: 72 PFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLP 131 P YFRNSLIV V+AL I GY+ A+Y+F + + T+ +PG+ LP Sbjct: 77 PVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLP 136 Query: 132 LYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCN 191 L++ + + TGI I++ L++ Y A VPF+IW+I GFF +P +L EAA+IDGC Sbjct: 137 LFMLYAR----TGI--IDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCT 190 Query: 192 KFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTA 251 + AF +V PLA PGI + I+ FLT+W+E A + + T+P G+ + A T Sbjct: 191 PWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTI 250 Query: 252 RYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + + A ++ +P L + F +QK +SG+T GAVKG Sbjct: 251 DWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG 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: 239 Number of extensions: 8 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: 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