Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate SMc02772 SMc02772 sugar ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Smeli:SMc02772 Length = 324 Score = 153 bits (386), Expect = 6e-42 Identities = 106/302 (35%), Positives = 158/302 (52%), Gaps = 13/302 (4%) Query: 10 ITIGVFVLGYLYCLTQFPGFASTRV-----ICNILTDNAFLGIIAVGMTFVILSGGIDLS 64 I G+ ++G L L G A+ I N+L A I+AVG TFVI++ GIDLS Sbjct: 19 ILFGLTLVGLLVVLWLLLGLATNAFWTPNNISNLLRQGAMTAILAVGQTFVIITAGIDLS 78 Query: 65 VGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGM 124 VG+V+ FT V +A ++ G+ LA L +G GAF I + +P FIITLA + Sbjct: 79 VGAVVGFTSVIVAWLLAA-GVPLWLAIIATLAIGVLIGAFHAFGIVRMGLPPFIITLATL 137 Query: 125 FFLRGVSYLVSEES-IPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRT 183 LRG+ L++ S I I + + T S + G S ++++ + +FL H + Sbjct: 138 TSLRGIGLLITNGSTISITNDAFTTFSRADFL----GIPSLFWMVIVVAIPAYVFL-HLS 192 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243 RFG ++A+G N+ +A L G++ T Y+LS+ A G++ + G A G Sbjct: 193 RFGRYLFAVGSNSEAARLSGVNVNRTIYLAYILSSTCAAFVGLLLASRIGIGNATQAEGW 252 Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFI 303 EL AIAS VIGGT L G VG+V G L G I I N ++S+W +I G+L+ + Sbjct: 253 ELQAIASSVIGGTSLFGAVGSVHGPLLGAFILATINNGANL-LNVNSFWQRIITGLLIIV 311 Query: 304 FI 305 + Sbjct: 312 IV 313 Lambda K H 0.329 0.145 0.428 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: 337 Number of extensions: 22 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: 331 Length of database: 324 Length adjustment: 28 Effective length of query: 303 Effective length of database: 296 Effective search space: 89688 Effective search space used: 89688 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: 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