GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas putida KT2440

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 PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Putida:PP_3817
          Length = 382

 Score =  234 bits (598), Expect = 2e-66
 Identities = 142/352 (40%), Positives = 201/352 (57%), Gaps = 17/352 (4%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           V L  + K +G   AV + +LE +DGEF+ F+G SG GK+TTL M+AG E  S G I + 
Sbjct: 15  VSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEILVD 74

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
            + + +VPP  RDI MVFQ Y+L+PH+NV +N+AF L +R+    E  +RV    +++++
Sbjct: 75  GQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLVQL 134

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           E   +RKP ++SGGQ+QRVA+ RA+V EP++ LMDEPL  LD KLR +++ E+ +L RRL
Sbjct: 135 EQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHRRL 194

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
           G+T +YVTHDQ EAM L  RI +   G+I  + T  +LY  P N FVA F+G  + NF+R
Sbjct: 195 GITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLG--NSNFLR 252

Query: 244 AGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKG-----YTTIP 298
                 G   +   P   IR    L       A ++  + VRPE              +P
Sbjct: 253 IKASSNGAGSFEGQP-VAIRLTPGLA------ASQDALIMVRPEKAVAMSAEQAMREPLP 305

Query: 299 EEENVLRGEVEVVEPLGAETEIH-VAVNGTLLVAKVDGHA--PVKPGDKVEL 347
              N +  +V  V  LG     H V   GT L  K    A  P++PGD V++
Sbjct: 306 AGWNEVTAKVGEVLFLGESQTCHVVTAGGTELTVKALSAAGMPMQPGDSVKV 357


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: 314
Number of extensions: 11
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: 376
Length of database: 382
Length adjustment: 30
Effective length of query: 346
Effective length of database: 352
Effective search space:   121792
Effective search space used:   121792
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.

Links

Downloads

Related tools

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