Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1059 Psest_1092 Branched-chain amino acid ABC-type transport system, permease components
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__psRCH2:GFF1059 Length = 295 Score = 136 bits (343), Expect = 5e-37 Identities = 91/297 (30%), Positives = 146/297 (49%), Gaps = 27/297 (9%) Query: 7 QLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP- 65 QLL GL G+ Y L+++G +++G++ +INFAHG +MLG F A F GL Sbjct: 15 QLLLGLINGAFYALLSLGLAIIFGLLRIINFAHGAQYMLGAFVA----------FLGLNY 64 Query: 66 VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGP 125 + V LV+A L+ IER R + G L L+ G+++ + G Sbjct: 65 LGVSYWFALVLAPLVVGCLGMAIERGLLRRIAGEDHLYGLLLTFGLALIVEGSFVKLFGV 124 Query: 126 RNK--PIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDR 183 P+P ++ + G + + + +IV V+ WY++ RT LG RA ++ Sbjct: 125 SGSSYPMPELLRGGFNLGFMFLPTYRAWVIVAALVVCLATWYVIERTRLGSYLRAGTENP 184 Query: 184 KMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPG------VKAFTA 237 K+ G+NV +++T+ G ALAA AG + Y V TPG + F Sbjct: 185 KLMQGFGINVPLLVTLTYGYGVALAAFAGVLAAPIYAV-------TPGMGSNLLIVVFAV 237 Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 V+GG+GS+ GA+ G+ +GLIE L ++ A V F ++ VL+ +P G+ G+ Sbjct: 238 VVIGGMGSILGAIVTGIAMGLIEGLTKVFYPEAANTV-VFLVMVAVLLIRPAGLFGK 293 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: 322 Number of extensions: 20 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: 300 Length of database: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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