Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS00195 RR42_RS00195 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Cup4G11:RR42_RS00195 Length = 309 Score = 174 bits (440), Expect = 3e-48 Identities = 100/310 (32%), Positives = 166/310 (53%), Gaps = 11/310 (3%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M Q + NGL LG IY +VA+G+T+ +G++ +I F+HGD M+G FA L + + Sbjct: 1 MSVIGQYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLML 60 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 P LL V+L A+ +T L I + PLR + L L+ + + + ++ Sbjct: 61 DIQSPWIRLLAVVLC-AICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRESVR 119 Query: 121 V--TQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177 + G KP P ++ + + G++S+ +I++ ++ ++ RT G A R Sbjct: 120 LFYPDGSNPKPFPALLPTASIELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGMAIR 179 Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237 A QD + A L+G+N + + +TF +G+ +AA+AG M +YY +FN G GV F A Sbjct: 180 AVAQDGETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIGFAA 239 Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTI-------AYKDVATFAILAFVLIFKPTG 290 A+LGG+G++ GA+ GG L ++ L SA AYKDV FA++ ++ +KPTG Sbjct: 240 AILGGLGNIYGAILGGFLFAALQVLGSATLPALIPDIPSAYKDVFAFAVVIVLMAWKPTG 299 Query: 291 ILGRPEVEKV 300 ++ E+V Sbjct: 300 LIAEKSSERV 309 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: 288 Number of extensions: 24 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: 309 Length adjustment: 27 Effective length of query: 273 Effective length of database: 282 Effective search space: 76986 Effective search space used: 76986 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