Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 139 bits (351), Expect = 6e-38 Identities = 95/277 (34%), Positives = 142/277 (51%), Gaps = 15/277 (5%) Query: 10 VFIHASALLLAVVILAPVAWLLIMSISPAADL---SAKPLAWWPSDIDLSRYRTLLSAVE 66 V I+ + V+L P W+ I + P +L SA P +W + ++ LL Sbjct: 27 VTIYIPLGIFVFVLLFPFYWMAITAFKPDGELLMRSANP--FWVMAPTFAHFKKLLF--- 81 Query: 67 NSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRT--PAVAWSLYAVIATYMLPPV 124 + LLN++ V+ ++T A++ +V AA+A+ R AV Y++PP Sbjct: 82 ---DTPYPEWLLNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPS 138 Query: 125 ALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARL 184 L +PL + GL ++ + L L Y T L PF TWLL F SIP E+E A+IDGA Sbjct: 139 ILFIPLASIVFQLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATR 198 Query: 185 DQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAI-ADLAGGRVS 243 +IL + LPLA P + ++ +FAF L+W+EF YAL F S KT+ V I +L G V Sbjct: 199 WEILVKIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDVY 258 Query: 244 DYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280 +G + +L +LP L+ +SG+T G VK Sbjct: 259 HWGALMAGALLGSLPVALVYSFFVEYYVSGMT-GAVK 294 Lambda K H 0.325 0.136 0.402 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: 206 Number of extensions: 7 Number of successful extensions: 2 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: 281 Length of database: 295 Length adjustment: 26 Effective length of query: 255 Effective length of database: 269 Effective search space: 68595 Effective search space used: 68595 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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