Align Inositol transport system permease protein (characterized)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 139 bits (349), Expect = 1e-37 Identities = 103/342 (30%), Positives = 162/342 (47%), Gaps = 44/342 (12%) Query: 23 AMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQISAQFMII---AVGACLLMI 79 ++I L + + V ++ + A D N + NW + Q I+ AVG +++ Sbjct: 23 SLIHSPLALPLAGLVVVSLLMGLASD----NFFTLSNWFNVLRQVSIVGILAVGMSFVIL 78 Query: 80 AGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSF 139 G DLSVG+ + AG + A V G P LA+L +AT IG LNG +V +P+ Sbjct: 79 TGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAI 138 Query: 140 IVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGW 199 IVTLA + + RG G I +G + G GW Sbjct: 139 IVTLATMGVARGV-------------------------------GLIYSGGYPISGLPGW 167 Query: 200 IAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGV 259 I+ F G R G V + MLIV+A+ ++L +T FG ++A GG+ AAR SGV Sbjct: 168 ISWFGVG-RIGMVPVPVILMLIVYAL-----AWLLLQRTAFGRHVYAIGGNEMAARLSGV 221 Query: 260 PVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGS 319 R+K+ ++ + F + + A + G+ E +AI AVV+GG + GG G Sbjct: 222 KTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGL 281 Query: 320 VLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVIL 361 V+G +GA++ G++ GL G+ L + G+I+L A+ + Sbjct: 282 VVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 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: 440 Number of extensions: 36 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: 373 Length of database: 328 Length adjustment: 29 Effective length of query: 344 Effective length of database: 299 Effective search space: 102856 Effective search space used: 102856 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