Align Inositol transport system permease protein (characterized)
to candidate SMa0070 SMa0070 ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Smeli:SMa0070 Length = 327 Score = 170 bits (431), Expect = 4e-47 Identities = 116/351 (33%), Positives = 172/351 (49%), Gaps = 52/351 (14%) Query: 26 RPELGGIIGTITVFAMFLIFAGDSGMF-----NSQGVMNWSQISAQFMIIAVGACLLMIA 80 +PEL G+ +F + L+F S N +GVM + + ++A+G LLMI Sbjct: 11 KPELAGLA---LLFVLVLVFQAKSNGILLSFENMRGVMG---LLPEMALVAIGVTLLMIC 64 Query: 81 GEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFI 140 GEFDLSVGS+ M +A+ + G P +A+L+ I AIG +NG++ ++ +PSFI Sbjct: 65 GEFDLSVGSVFALMPMSMAVL-LNSGVPFTVAVLLGLMICGAIGFINGYVTLQFSIPSFI 123 Query: 141 VTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGD---WLAALFGGKILTGLFQWFGDN 197 TL LFI R I I GG D WL F D Sbjct: 124 TTLGMLFIARSLTI---------VISGGFPPLLPPDLPTWL---------------FTDY 159 Query: 198 GWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNS 257 W +G P M +W +++ + +L+ T FGNWI A GG EAA + Sbjct: 160 IW---------QGSP----FRMSFLWFVVIAALVAALLSLTNFGNWIRATGGFNEAAASM 206 Query: 258 GVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGY 317 G+PV RVKI+ FM + A QV+ G G E +A+ A VIGG L GG Sbjct: 207 GIPVKRVKIVCFMLCSVLAGFAGLLQVLRLGSPLPSIGEGLELQAVAAAVIGGTALAGGI 266 Query: 318 GSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIRRV 368 G+V GA +G L+ + GL + V+++ F+ +G++ +FAVI N ++ ++ Sbjct: 267 GTVFGAIIGTLLIRTIDNGLVLSRVDANWFKFAIGVLTMFAVIANAWMGKM 317 Lambda K H 0.330 0.145 0.443 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: 449 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 373 Length of database: 327 Length adjustment: 29 Effective length of query: 344 Effective length of database: 298 Effective search space: 102512 Effective search space used: 102512 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: 49 (23.5 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