GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dechlorosoma suillum PS

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 Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__PS:Dsui_2943
          Length = 356

 Score =  203 bits (516), Expect = 7e-57
 Identities = 134/364 (36%), Positives = 198/364 (54%), Gaps = 21/364 (5%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA + L  V +R+G    V       E G     +GPSGCGKTT LR IAG E+I+ G+I
Sbjct: 1   MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60

Query: 61  YIGDRLVN----DVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKE 116
            +   LV+     + P+ R I MVFQ+YAL+PH+ V +N+AFGL+ +     E  +RV  
Sbjct: 61  ALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRVAA 117

Query: 117 AARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEI 176
              ++ +     + P ELSGGQ+QRVA+ RA+   P++ L+DEP SNLD  LR  +  E+
Sbjct: 118 MLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEV 177

Query: 177 AKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS 236
            ++ ++ G T I VTHDQ EA  +   I VM +G IQQ DTP NLY  PANRFVA F+G 
Sbjct: 178 REILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVGQ 237

Query: 237 PSM--NFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGY 294
                  V AG  VQ E + ++  G  +  +A  G   K   G  V + +RP+ +     
Sbjct: 238 GVFVPGTVLAGNRVQME-LGILESGVPVECSAGCGVCGK---GCGVDILLRPDDV----- 288

Query: 295 TTIPEEENVLRGEVEVVEPLGAETEIHVAV-NGTLLVAKVDGHAPVKPGDKVELLADTQR 353
             + ++++ L+  VE     GA+    + + +G  +++ V  H     G+K+ +  D   
Sbjct: 289 --VHDDKSPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLDVDH 346

Query: 354 LHAF 357
           + AF
Sbjct: 347 VVAF 350


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: 335
Number of extensions: 12
Number of successful extensions: 3
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: 356
Length adjustment: 30
Effective length of query: 346
Effective length of database: 326
Effective search space:   112796
Effective search space used:   112796
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