Align Inner-membrane translocator (characterized, see rationale)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 159 bits (401), Expect = 1e-43 Identities = 106/301 (35%), Positives = 162/301 (53%), Gaps = 16/301 (5%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L+ + LV D F + ++N+ R + I A+GMT VI++GGIDLSVG V+ALSG Sbjct: 38 LVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVILTGGIDLSVGPVMALSGT 97 Query: 76 VTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTL 135 +T+ L+ P LA + +G FG G + + P IVTLA M +ARGL Sbjct: 98 LTAGLMVA-GLPPGLAIGAGMLIGVAFGIGNGLFVAYLHMPPIIVTLATMGIARGLGLMY 156 Query: 136 SEESIAIDHP----FYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVY 191 ++ P F+ + I +P LI +L +++ V++ +TR G +Y Sbjct: 157 TDGYPISGLPDWFAFFGRESLFGIQVP--------ILIMLLTYLVAYVLLQHTRIGRYIY 208 Query: 192 AIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAA 251 AIGGN+ + L G+ A+ + +Y IS A +AG+V T SG + ELDAIAA Sbjct: 209 AIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAGVSFELDAIAA 268 Query: 252 VVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIG--LLLFFFILLQ 309 VV+GG + GG G ++GT+LG +L+GV+ + G +S + ++ G +LL FI Q Sbjct: 269 VVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLG-VSPYVQSVIKGGIILLAIFISRQ 327 Query: 310 K 310 + Sbjct: 328 R 328 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: 349 Number of extensions: 18 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: 330 Length adjustment: 28 Effective length of query: 292 Effective length of database: 302 Effective search space: 88184 Effective search space used: 88184 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: 48 (23.1 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