Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate Ac3H11_2065 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= TCDB::Q97UY9 (287 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2065 Length = 289 Score = 132 bits (332), Expect = 9e-36 Identities = 85/290 (29%), Positives = 142/290 (48%), Gaps = 19/290 (6%) Query: 7 PVIKASLHYLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLS 66 P + L Y LA+ + +L+P+YAML+ FK E+ ST +L P + + A+ + S Sbjct: 9 PSVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWSAWGTAWQS 68 Query: 67 ---------LAKPLINSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSL 117 L +NS+ + +P IS GA+ Y + S D LF + Sbjct: 69 ACTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGS-------DALFGM 121 Query: 118 ISLATFIPQEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLI 177 + F+P + LLP+++++ +GL S G++ + + L + + IP+ L+ Sbjct: 122 LLFGVFMPFQVVLLPMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELV 181 Query: 178 EAAKMDGTGDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMKLT-SIA 236 AA+MDG +IF +IV PLS P + TLI+ WN+F +V T +T + Sbjct: 182 NAARMDGASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGLN 241 Query: 237 VLSYSGAYGTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286 L+ + + YN AA ++A + + I+V G++F+RGL A G KG Sbjct: 242 NLANTSSSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTA--GAVKG 289 Lambda K H 0.330 0.144 0.417 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: 227 Number of extensions: 15 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: 287 Length of database: 289 Length adjustment: 26 Effective length of query: 261 Effective length of database: 263 Effective search space: 68643 Effective search space used: 68643 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 (21.8 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