Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate BWI76_RS26300 BWI76_RS26300 glycerol-3-phosphate transporter permease
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__Koxy:BWI76_RS26300 Length = 295 Score = 113 bits (283), Expect = 5e-30 Identities = 84/279 (30%), Positives = 138/279 (49%), Gaps = 13/279 (4%) Query: 17 WLFVAPALGLITLFMVYPIAWSLWMSFQSGR--GMTLKFAGFANIVRLWNDPVFIKALTN 74 +L VAP L + +F ++P +LW S QS G++ +F G N + L+ DP ++ + Sbjct: 15 YLLVAPQLVITVIFFIWPAGEALWYSLQSVDPFGLSSQFVGLDNFLALFQDPYYLDSFWT 74 Query: 75 TMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD 134 T+ + + +L++L A+L++ + G ++T + LP + +VL+ +F Sbjct: 75 TIKFSTMVTVSGLLISLFFAALVDYV-VRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNPG 133 Query: 135 -GIVNSTLQAIGLAASPIPW--LTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSI 191 G++ L +G W + A LV+ A W+ YN +F+ AALQ+I +S+ Sbjct: 134 RGLITHLLGEMGY-----DWNHAQNSGQAMFLVVFASVWKQISYNFLFFFAALQSIPRSL 188 Query: 192 YEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATL 251 E A IDG R L +PL+ PV F V++ + V + G GGP AT Sbjct: 189 VEAAAIDGAGPVRRFFRLALPLIAPVSFFLLVVNLVYAFFDTFPVIDAATG-GGPVQATT 247 Query: 252 TLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290 TL IY F + +L +A S V++ LV +L VQF Sbjct: 248 TLIYKIYREGFAGL-DLSASAAQSVVLMFLVIILTVVQF 285 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: 243 Number of extensions: 14 Number of successful extensions: 4 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: 295 Length adjustment: 26 Effective length of query: 272 Effective length of database: 269 Effective search space: 73168 Effective search space used: 73168 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 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