Align putative transporter, required for L-alanine utilization (characterized)
to candidate RR42_RS04305 RR42_RS04305 membrane protein
Query= reanno::MR1:202450 (213 letters) >FitnessBrowser__Cup4G11:RR42_RS04305 Length = 213 Score = 133 bits (335), Expect = 2e-36 Identities = 70/193 (36%), Positives = 117/193 (60%), Gaps = 3/193 (1%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVENVHYLIA 71 ++G+LA A++G + A +++ D G ++ ATA GGGT+RD+LL P WV++ Y+I Sbjct: 21 VVGVLAFAVSGVVDARKQRFDAVGTFVVAFATAFGGGTVRDVLLDRRPFYWVDHEGYVIL 80 Query: 72 IAFASL-LTVAIAPVMRYLS-KLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVT 129 I SL + + V R S + + DA+GL +FS+ G L+ +PT+AV+MG+++ Sbjct: 81 IFVMSLGASFVLRVVSRVASERTMITADAIGLGLFSVTGTSLALVAQMTPTVAVMMGIIS 140 Query: 130 GVFGGVIRDILCNQVPLIFK-KELYAVISLFTAGLYITLNAYQLEEWINLVICLTLGFSL 188 VFGGV+RD+LCN+VP+I + + YA + +YI L Q E+ + L+ + Sbjct: 141 SVFGGVVRDVLCNEVPMILRDRSPYATCAFVGCCVYIGLTWLQAEQELALLAGAITITAA 200 Query: 189 RMLALRYHWSMPT 201 R+L +R+ W +P+ Sbjct: 201 RLLCVRFGWKLPS 213 Score = 30.0 bits (66), Expect = 3e-05 Identities = 18/79 (22%), Positives = 33/79 (41%) Query: 85 VMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQV 144 +M L + ++ +G+ F++ G F V+ T GG +RD+L ++ Sbjct: 8 LMGRLPLILHVMEVVGVLAFAVSGVVDARKQRFDAVGTFVVAFATAFGGGTVRDVLLDRR 67 Query: 145 PLIFKKELYAVISLFTAGL 163 P + VI +F L Sbjct: 68 PFYWVDHEGYVILIFVMSL 86 Lambda K H 0.330 0.143 0.436 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: 147 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 213 Length of database: 213 Length adjustment: 22 Effective length of query: 191 Effective length of database: 191 Effective search space: 36481 Effective search space used: 36481 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: 45 (21.9 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