Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate WP_037152734.1 RHSP_RS17900 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21653 (298 letters) >NCBI__GCF_000359745.1:WP_037152734.1 Length = 308 Score = 157 bits (397), Expect = 3e-43 Identities = 98/300 (32%), Positives = 171/300 (57%), Gaps = 11/300 (3%) Query: 1 MVRARRGIGRYYDVNGW---LFVAPALGLITLFMVYPIAWSLWMSFQSGRGM-TLKFAGF 56 + R R +++ GW F+ P L I LF+V PI S+ +SF + + + T +F GF Sbjct: 9 IARPRPRSRKWFRGEGWTALFFLLPGLIGIVLFLVLPILASIALSFTNWQLLGTPRFVGF 68 Query: 57 ANIVRLWN-DPVFIKALTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLP 115 +N +RL+ DP F L NT+ + V + + I+++L LA+ +++ + +G+ FR FLP Sbjct: 69 SNYLRLFTTDPQFWTVLRNTLFFTVEYLVLNIVISLGLATWISSLK-IGQRWFRVIFFLP 127 Query: 116 CVSSLVAYSVLFKGMFATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGY 175 + L+A ++++ +F + G+ ++ + A+ L S + L A V+L W GY Sbjct: 128 TFTPLIAVAMVWMLIFTSGGLFDNLMAALSLPFSGV--LNDRALAMQAVVLTSIWAGVGY 185 Query: 176 NMIFYLAALQNIDKSIYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDE 235 N + + AAL + + E ARIDG AW R + +PL+ P + F TV++ I +LQ+FD+ Sbjct: 186 NTVLFNAALDMVPATYLEAARIDGATAWDRFWKIRLPLISPTLFFGTVMTAITSLQVFDQ 245 Query: 236 VYNLTEGKGGPSNATLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAARE 295 ++ +T KGGP ++T TL IY F+ +GYA+ +++V+ L+ L +QF+ R+ Sbjct: 246 IFVMT--KGGPGSSTATLGYAIYQRGFQNF-QMGYASAIAWVMFALIMALTALQFWFQRK 302 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: 306 Number of extensions: 19 Number of successful extensions: 6 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: 308 Length adjustment: 27 Effective length of query: 271 Effective length of database: 281 Effective search space: 76151 Effective search space used: 76151 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