Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate PfGW456L13_3040 Various polyols ABC transporter, permease component 2
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3040 Length = 276 Score = 135 bits (339), Expect = 1e-36 Identities = 86/282 (30%), Positives = 148/282 (52%), Gaps = 10/282 (3%) Query: 1 MERQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRT 60 +++ L S+ + A +A++I P+ W+++ S D A P P I + Sbjct: 3 LQQSRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATP----PQFIFMPTLEN 58 Query: 61 LLSAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVS--RTPAVAWSLYAVIAT 118 L E S +F NS+ ++ AT +++AVPAA++++ T +L +++T Sbjct: 59 YLHINERSDYFSFA---WNSVVISFSATALCLLIAVPAAYSMAFYETQRTRGTLLWMLST 115 Query: 119 YMLPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAM 178 MLPPV + +P+Y+ FGLL++ L ++Y I P W++ + F IPR+I AA Sbjct: 116 KMLPPVGVLMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPRDILEAAR 175 Query: 179 IDGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLA 238 +DGA L Q + + LP+A +A++ L + +L W+E F++L TS +A LT IA + Sbjct: 176 LDGATLAQEMLRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTS-SKAAPLTALIASYS 234 Query: 239 GGRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280 + ++ LA P ++ G I Q+ L+ GL+ G VK Sbjct: 235 SPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 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: 212 Number of extensions: 8 Number of successful extensions: 1 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: 276 Length adjustment: 25 Effective length of query: 256 Effective length of database: 251 Effective search space: 64256 Effective search space used: 64256 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 Apr 09 2024. 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