Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate YP_004141675.1 Mesci_2480 binding-protein-dependent transport system inner membrane protein
Query= reanno::Smeli:SM_b21653 (298 letters) >NCBI__GCF_000185905.1:YP_004141675.1 Length = 311 Score = 160 bits (406), Expect = 3e-44 Identities = 106/303 (34%), Positives = 162/303 (53%), Gaps = 11/303 (3%) Query: 2 VRARRGIGRYYDVNG---WLFVAPALGLITLFMVYPIAWSLWMSFQSGRGMT-LKFAGFA 57 V +R G R+ +G ++ + PA L LF ++P W+S + G + +AGF+ Sbjct: 11 VSSRSGTWRFDAGDGATAFVMILPAAILFGLFYLWPFVNGFWLSLHNWDGFSDPTWAGFS 70 Query: 58 NIVRLWNDPVFIKALTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCV 117 N +RL +D F+ AL N + + V V + L L LA LLN L+GR FR A F+P Sbjct: 71 NYMRLAHDRTFLGALRNNLIFVVAVVVLKNALGLGLALLLNRA-LLGRAFFRAAAFIPVT 129 Query: 118 SSLVAYSVLFKGMF-ATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYN 176 S VA +L+ ++ G++NS L IGLA WL A +I+ W+W G++ Sbjct: 130 MSFVAVGLLWSWIYNPVFGLLNSGLDLIGLAGLKRSWLGDADIALYSIIVVDVWKWLGFH 189 Query: 177 MIFYLAALQNIDKSIYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGT-LQLFDE 235 + YLA LQ I +YE A++DG R H+T+P++ P+I T++ G ++ FD Sbjct: 190 AVIYLAGLQTIPSELYESAKMDGAGPLQRFRHVTVPMMTPIIFINTILGLSGAFVRNFDI 249 Query: 236 VYNLTEGKGGPSNATLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAARE 295 VY LT KGGP++AT + Y+ + F+ + YAA + YV+ ++V LA V A Sbjct: 250 VYVLT--KGGPNHATEVVLTYMMSKAFQ-DGAMSYAAAIGYVLFMIVG-LASVGLLALMR 305 Query: 296 RDR 298 R R Sbjct: 306 RQR 308 Lambda K H 0.330 0.142 0.447 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: 267 Number of extensions: 17 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: 298 Length of database: 311 Length adjustment: 27 Effective length of query: 271 Effective length of database: 284 Effective search space: 76964 Effective search space used: 76964 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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