Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate AO353_20825 AO353_20825 ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20825 Length = 325 Score = 198 bits (503), Expect = 2e-55 Identities = 121/307 (39%), Positives = 178/307 (57%), Gaps = 7/307 (2%) Query: 33 LGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSI 92 LG+ L+ + FSVL+ +F + S +A Q MVLA GMTFV++ GGIDLSVGS+ Sbjct: 21 LGLAGALLAMIALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSV 80 Query: 93 LSISAVVAMLVSLMPQLGMLSVPAALL---CGLLFGIVNGALVAFMKLPPFIVTLGTLTA 149 L+++ + L G +PAALL + G + G++ ++P FIV+LG L Sbjct: 81 LALAGSTVSVAIL--GWGWSVLPAALLGMAAAAVAGTITGSITVAWRIPSFIVSLGVLEM 138 Query: 150 VRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIY 209 RG+A + T Y D FA++ N G+ IIA V+ ++ VL RTV G + Sbjct: 139 ARGVAYQMTGSRTAYIGD-AFAWLSNPITFGISPSFIIALLVIFIAQAVLTRTVFGRYLI 197 Query: 210 AVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIA 269 +G N EA RL+GI + V+++ GLLAG+ + +RL AA+ G EL IA Sbjct: 198 GIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADP-NAGSGLELQVIA 256 Query: 270 AVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSY 329 AV++GGTS +GG GS++ T G LII+VL+ GL +G ++ + II G VI+ AV LD+Y Sbjct: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316 Query: 330 RRKGSAR 336 R + ++R Sbjct: 317 RSQRASR 323 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: 371 Number of extensions: 26 Number of successful extensions: 5 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: 325 Length adjustment: 28 Effective length of query: 309 Effective length of database: 297 Effective search space: 91773 Effective search space used: 91773 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