GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Rhizobium freirei PRF 81

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate WP_004127659.1 RHSP_RS29490 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000359745.1:WP_004127659.1
          Length = 362

 Score =  345 bits (885), Expect = 1e-99
 Identities = 188/367 (51%), Positives = 254/367 (69%), Gaps = 11/367 (2%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA++ L ++ KR+G +  +   NLE +DGEFVVFVGPSGCGK+T LRMIAGLE+IS G +
Sbjct: 1   MAELSLTNIVKRYGSLEIIHGANLEVKDGEFVVFVGPSGCGKSTLLRMIAGLEDISGGEL 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            IG R+VND  P DR IAMVFQ+YALYPH+ V +N+ FGLR+   PK + DRRVK+AA I
Sbjct: 61  KIGGRVVNDAEPADRGIAMVFQSYALYPHLTVEQNLNFGLRMNGNPKADTDRRVKQAAEI 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L+I  L+ R+P++LSGGQRQRVA+GRAIVREP++FL DEPLSNLDA+LRV+MR EI++L 
Sbjct: 121 LQITELMQRRPKQLSGGQRQRVAIGRAIVREPQIFLFDEPLSNLDAELRVQMRVEISRLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           ++LG T IYVTHDQ EAMTL  +IVV++ G I+QV  PL+LYD PAN+FVAGF+GSP MN
Sbjct: 181 KKLGTTMIYVTHDQTEAMTLADKIVVLRSGNIEQVGAPLDLYDDPANQFVAGFVGSPKMN 240

Query: 241 FVRAG-VEVQGEKVYLVAPGFR-IRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIP 298
           F++A  V+VQ  +  +V    R +R    + SA K   G++V +GVRPEH     +    
Sbjct: 241 FLQAEVVDVQPGRAIIVMKSQRNVRLTLAVTSA-KIEIGQQVTIGVRPEH-----FLDAG 294

Query: 299 EEENVLRGEVEVVEPLGAETEIH--VAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHA 356
             +  L  +V+V E LG  + I+  +A N  +++ + +        DK+ +     +   
Sbjct: 295 RGDADLTVDVDVAEHLGNTSYIYANIAANEQIVIEREESRT-TGNSDKLTVALSAAKTFL 353

Query: 357 FDLETDR 363
           FD   +R
Sbjct: 354 FDSAGNR 360


Lambda     K      H
   0.320    0.139    0.400 

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: 388
Number of extensions: 13
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: 376
Length of database: 362
Length adjustment: 30
Effective length of query: 346
Effective length of database: 332
Effective search space:   114872
Effective search space used:   114872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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