Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__PS:Dsui_0629 Length = 307 Score = 261 bits (667), Expect = 1e-74 Identities = 143/308 (46%), Positives = 204/308 (66%), Gaps = 11/308 (3%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M+ F+QQ++NGL LGSIY LVA+GYTMVYGI+G+INFAHG++ M+G AL V +L Sbjct: 1 MDIFLQQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGALTALTVVKLLAG- 59 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 +GLP V+ L+ L+ A + + IE++AYRPLR + RLAPLITAIG+SI L N Sbjct: 60 -SGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLRKAPRLAPLITAIGVSIVLQNLAM 118 Query: 121 VTQGPRNKPIPPMV-SSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 + G P ++ + ++ + + Q+II+++ A ++ ++NRT LGRA RAT Sbjct: 119 MVWGRSYHSFPAVLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMRAT 178 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 ++ +A L+GVNV+ IS+TFV+G+ALAAVAG M Y +A + GF G+KAFTAAV Sbjct: 179 AENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTAAV 238 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVLIFKPTGI 291 LGGIG+L GA+ GG+L+GLIESL + Y Y+DV F +L VL+F+P+G+ Sbjct: 239 LGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPSGL 298 Query: 292 LGRPEVEK 299 +G E+ Sbjct: 299 VGEKVAER 306 Lambda K H 0.329 0.143 0.421 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: 380 Number of extensions: 21 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: 300 Length of database: 307 Length adjustment: 27 Effective length of query: 273 Effective length of database: 280 Effective search space: 76440 Effective search space used: 76440 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