Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 150 bits (380), Expect = 3e-41 Identities = 106/312 (33%), Positives = 167/312 (53%), Gaps = 20/312 (6%) Query: 7 IPLWITASLL---LTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63 +P+ + LL LT++L G FAS N+LR A L+ A GMT VI++ GID Sbjct: 30 LPVLVVLYLLFYGLTLYLSGDGT-SNFASAENTMNILRQVAINLVLAAGMTFVILTAGID 88 Query: 64 LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123 LSVG+V+A+S V+ + P A + + G + G + G ++ + + F+VTL Sbjct: 89 LSVGSVLAVSAVLG--MQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLG 146 Query: 124 GMFLARGLATTLSEESIAI--DHPFYDAVAEMSIALPGNGA-LDLSSLIFILFFVIIA-- 178 M RG A L++ + + D P ++ + GNG L + LI++ V++ Sbjct: 147 TMTAFRGAAYLLADGTTVLNNDIPSFEWI--------GNGDFLHVPWLIWVAVAVVLLSW 198 Query: 179 VVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYA 238 V++ T G ++YAIGGN +A L GI + + +Y+IS + LAG + + Sbjct: 199 VILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANG 258 Query: 239 LGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVI 298 G ELDAIAAVV+GGT L GG G + GTV+G +++GV+ +T G LSS+W + Sbjct: 259 NWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILG-LSSFWQYVAK 317 Query: 299 GLLLFFFILLQK 310 G ++ ++L K Sbjct: 318 GAVIVLAVILDK 329 Lambda K H 0.330 0.145 0.424 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: 357 Number of extensions: 19 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: 320 Length of database: 339 Length adjustment: 28 Effective length of query: 292 Effective length of database: 311 Effective search space: 90812 Effective search space used: 90812 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