GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Burk376:H281DRAFT_02629
          Length = 381

 Score =  328 bits (840), Expect = 2e-94
 Identities = 191/383 (49%), Positives = 248/383 (64%), Gaps = 23/383 (6%)

Query: 1   MAKVRLEHVWKRF-GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59
           MA + L  + K F G    ++D NLE  + EF VF+GPSGCGK+T LR++AGLE+ ++G+
Sbjct: 1   MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60

Query: 60  IYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR 119
           + IG R +N VP  +R +AMVFQ+YAL+PHM VYENMAFGL+L R PK EIDR+V+EAA 
Sbjct: 61  VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120

Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179
           +L+++ LL RKPRELSGGQRQRVA+GRAIVREP VFL DEPLSNLDA LR + R EIA+L
Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180

Query: 180 -QRRLGVTTIYVTHDQVEAMTLGHRIVVM-------KDGEIQQVDTPLNLYDFPANRFVA 231
            QR    + +YVTHDQ+EAMTL  +IV++       + G I Q+  PL LY  P ++FVA
Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240

Query: 232 GFIGSPSMNFVRAGVE-VQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLG 290
           GFIGSP MNF+   VE +  + V +  PG  +R   V G  LKP  G+ V LG+RPEH+ 
Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSMPGTALRV-LVDGRRLKP--GQRVTLGIRPEHVR 297

Query: 291 LKGYTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLAD 350
             G T        L     + E LG  + +H    G  L+AK  G   V+ G+++ L   
Sbjct: 298 FDGGT------QTLAVNALLTEQLGEHSYLHADHAGGTLIAKAPGDLHVRNGERLALHLP 351

Query: 351 TQRLHAFD---LETDRTI-GHAQ 369
               H FD   +   RTI G+AQ
Sbjct: 352 ADACHLFDEDGIALHRTIVGNAQ 374


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: 428
Number of extensions: 18
Number of successful extensions: 5
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: 381
Length adjustment: 30
Effective length of query: 346
Effective length of database: 351
Effective search space:   121446
Effective search space used:   121446
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: 50 (23.9 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