Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate WP_008815659.1 M988_RS00265 sn-glycerol-3-phosphate ABC transporter permease UgpA
Query= SwissProt::O51924 (295 letters) >NCBI__GCF_001655005.1:WP_008815659.1 Length = 295 Score = 139 bits (349), Expect = 1e-37 Identities = 86/283 (30%), Positives = 142/283 (50%), Gaps = 9/283 (3%) Query: 11 YREAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSARE 70 ++ + L Y ++ P L + +F + P W S+ F FVG +N++ + Sbjct: 8 FKRSWLPYALVAPQLLITAIFFLWPAGEALWYSVQSLDPFGLSSEFVGWQNFITLWHDPY 67 Query: 71 FWYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWE 130 + + T+ FS + +L L FA ++N L+GR + + ++P+AV I+A W Sbjct: 68 YLSAFRTTLWFSGLVTFFGLVLSLFFAALVNHILRGRRFYQTLFILPYAVAPTIAAVLWM 127 Query: 131 LMYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIPQ 190 ++N GL + L ++G S N A F +V+A VWK + L LA LQ++P+ Sbjct: 128 FLFNPGLGLVSHFLGVMGYS-WNHAQNSGQAMFLVVLASVWKQVSYNFLFFLAALQSVPK 186 Query: 191 DLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDA-LRVFDIIYVLTGGGPGGAT 249 L EAA IDGA RF I LPL+ PV L++ + A F +I TGGGPG +T Sbjct: 187 SLLEAAAIDGAGPIRRFFHIVLPLISPVSFFLLVVNLVYAFFDTFPVIDAATGGGPGQST 246 Query: 250 TSISLLAFNYYNLG----DYGIGSAISILTFVLVLSFTIVYLK 288 T+ L + Y G D +A S++ ++V++ T++ + Sbjct: 247 TT---LIYKIYREGFAGLDLSSSAAQSVVLMLIVVALTMIQFR 286 Lambda K H 0.329 0.145 0.439 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: 237 Number of extensions: 18 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: 295 Length of database: 295 Length adjustment: 26 Effective length of query: 269 Effective length of database: 269 Effective search space: 72361 Effective search space used: 72361 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 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