Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3451 PS417_17665 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__WCS417:GFF3451 Length = 286 Score = 149 bits (377), Expect = 6e-41 Identities = 86/296 (29%), Positives = 157/296 (53%), Gaps = 14/296 (4%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 + ++ Q+LNGL LG IY L+++G T+++G++ +NFAHG F+LG + + S+ Sbjct: 2 LNLYLFQILNGLGLGMIYFLISVGLTIIFGLLNFVNFAHGAFFLLGAY----ICYTAVSL 57 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 +A+L+ ++V A+ W IERV + + + ++ +G+++ + Sbjct: 58 TGNFWLALLIAPLVVAALA------WVIERVLIQRIYHLPHMFQILVTLGIALIIQEASV 111 Query: 121 VTQGPRNK--PIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178 + GP K +P ++ V G+ ++ +IV + ++ W ++ RT G RA Sbjct: 112 MIWGPVGKSVAVPELLRGVLVVGDFVYPYYRLFLIVFSGLVGLGLWLLLERTRFGALVRA 171 Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238 + + +LLG N+ + S+TF +G ALA VAG ++ G F GV AF Sbjct: 172 GSESTETVSLLGTNIFRLFSMTFALGVALAGVAGVLFAPLRGAQPFVGPEILGV-AFVVV 230 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 V+GG+GS GA+ GGLL+G+++SL + + + + +A V++ +P G+ GR Sbjct: 231 VIGGMGSFSGALVGGLLVGVVQSLMTTLWPQG-ASLMIYGAMAVVILVRPYGLFGR 285 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: 310 Number of extensions: 22 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: 286 Length adjustment: 26 Effective length of query: 274 Effective length of database: 260 Effective search space: 71240 Effective search space used: 71240 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