Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SMc04136 SMc04136 ABC transporter permease
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__Smeli:SMc04136 Length = 315 Score = 149 bits (377), Expect = 6e-41 Identities = 96/270 (35%), Positives = 154/270 (57%), Gaps = 12/270 (4%) Query: 8 AGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRG--VGSFEFAGLDNFKSVIASN-SYRLAV 64 AGY+F P+L GF P+ S+Y FT + + E+ G N+ + ++ + AV Sbjct: 31 AGYMFLLPWLIGFFGLTLGPAIASLYLSFTNFDLIRAPEWIGTANYARIATADPKFAAAV 90 Query: 65 KNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVA-SIILVWQITFN 123 K T ++ +SVP + +LL+A+LL++ +RG +R F LP ++ + +I ++W+ F Sbjct: 91 KVTFLYVVLSVPFKLAFALLVAILLDRGVRGLTVYRAIFYLPSLLGGSVAIAVLWRQLFA 150 Query: 124 EFGVLNNLLNHFGIAGVEWLNSK-WSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYDA 182 G++N+LL FGI G W++ +SI LV+L VW+ G +I+F AGL IP D Y+A Sbjct: 151 GDGLINSLLAQFGIEGPSWISHPDYSIWTLVVLSVWQ-FGSPMIIFLAGLRQIPTDMYEA 209 Query: 183 ASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNY-PPLN--MYML 239 AS+DGA F+ F ITLPLL P IFF ++ I++FK F A+++ G P+N ++ Sbjct: 210 ASLDGASKFRQFYKITLPLLTPVIFFNAVVQTIDAFKAFTPAFIISGGTGGPINSTLFYT 269 Query: 240 QHFMNNNFNNLNYQRLSTASLLMELFIVAI 269 + F N R+ AS L + ++ I Sbjct: 270 LYLYQEAFGNF---RMGYASALAWILVLII 296 Lambda K H 0.331 0.144 0.444 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: 273 Number of extensions: 13 Number of successful extensions: 4 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: 284 Length of database: 315 Length adjustment: 27 Effective length of query: 257 Effective length of database: 288 Effective search space: 74016 Effective search space used: 74016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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