GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Phaeobacter inhibens BS107

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 GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  326 bits (836), Expect = 5e-94
 Identities = 188/362 (51%), Positives = 238/362 (65%), Gaps = 19/362 (5%)

Query: 1   MAKVRLEHVWKRFGK-VVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59
           MA+V L  V K +   V AV   + + EDGEFVV VGPSGCGK+T LRMIAGLE+I+EG 
Sbjct: 1   MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60

Query: 60  IYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR 119
           + IGDR+VN+V P DRDIAMVFQNYALYPHM V +N+A+GL+ R+ P+ EI ++V EAA+
Sbjct: 61  LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAK 120

Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179
           +L +E  L+RKP +LSGGQRQRVAMGRAIVR+P +FL DEPLSNLDAKLR +MR EI  L
Sbjct: 121 MLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKAL 180

Query: 180 QRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSM 239
           QRRLGVT+IYVTHDQVEAMT+  RI+V+  G I+Q+ TP  +Y  PA+ FVA F+G+P M
Sbjct: 181 QRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPM 240

Query: 240 NFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPE 299
           N + A           +A G     + V   AL   A   V LG+RPE + L        
Sbjct: 241 NLLDA----------TIANGQVTLPDGVSMGALDTSAQGAVKLGIRPEDVQLVA------ 284

Query: 300 EENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDL 359
            E  L  +VE++E LGA   +H  + G      V    PV PG   ++  D   +  FD 
Sbjct: 285 -EGGLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPGTH-QISVDPAAICLFDA 342

Query: 360 ET 361
           E+
Sbjct: 343 ES 344


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: 376
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: 348
Length adjustment: 29
Effective length of query: 347
Effective length of database: 319
Effective search space:   110693
Effective search space used:   110693
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 17 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