Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 213 bits (541), Expect = 7e-60 Identities = 127/327 (38%), Positives = 195/327 (59%), Gaps = 12/327 (3%) Query: 2 HESITRPAASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSI 61 H++ PAAS A + + L G++ V +L+ + ++NF N Sbjct: 3 HDANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLM----GLASDNFFTLSNWFN 58 Query: 62 IAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCG 121 + +Q SI +LA GM+FVILTGGIDLSVG+ ++++ ++ L+ G L P ALLCG Sbjct: 59 VLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTIS--AGLIVNSG-LPAPLALLCG 115 Query: 122 L----LFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGE 177 + G++NGALVA+ ++P IVTL T+ RG+ + I ++ G G Sbjct: 116 VGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGR 175 Query: 178 VLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSG 237 + VP VI+ V A++W +L+RT G +YA+GGN AARLSG+K + L VYA+SG Sbjct: 176 IGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISG 235 Query: 238 LLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAV 297 +GL ++ + RL + G +ELDAIAAV+LGGT+ GG G +VGTL+GA+++ + Sbjct: 236 FTSGLAAIILTGRLMSGQP-NAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGI 294 Query: 298 LSNGLVLLGVSDIWQYIIKGLVIIGAV 324 L+NGL L+G++ Q II+G++I+ A+ Sbjct: 295 LNNGLNLMGINPYLQDIIRGVIILLAI 321 Lambda K H 0.325 0.141 0.409 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: 391 Number of extensions: 21 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: 337 Length of database: 328 Length adjustment: 28 Effective length of query: 309 Effective length of database: 300 Effective search space: 92700 Effective search space used: 92700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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