GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Pseudomonas putida KT2440

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate PP_5179 PP_5179 spermidine/putrescine ABC transporter - ATP binding subunit

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__Putida:PP_5179
          Length = 380

 Score =  235 bits (600), Expect = 1e-66
 Identities = 138/340 (40%), Positives = 199/340 (58%), Gaps = 24/340 (7%)

Query: 6   VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65
           V ++ VTK ++ + VAV + +L +   E   LLG SG GK+T LRM+AG E  ++G+I++
Sbjct: 23  VKIDRVTKKFD-ETVAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFERPSEGRIFL 81

Query: 66  DGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILG 125
           DG  + D+ P +R I M+FQ+YAL+PHMTV +N+AFGL+  K PK EID RV E  K++ 
Sbjct: 82  DGVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLQQDKMPKAEIDARVAEMLKLVH 141

Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185
           +     RKP QLSGGQRQRVA+ R++ + PK+ L DEP+  LD KLR QM+ EL ++  R
Sbjct: 142 MTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIER 201

Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFV 245
           +  T + VTHDQ EAMTMA +I +M  G I QIG+P +IY +P +  V  FIG+      
Sbjct: 202 VGVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYETPTSRLVCEFIGN------ 255

Query: 246 NARVVRGEGGLWIQASGFKVKVPKEFEDKL-------ANYIDKEIIFGIRPEDIYDKLFA 298
              V   EG +   A G+ +    E E K+        +  DK I + +RPE    K+  
Sbjct: 256 ---VNLFEGDVVDDAEGYAIIASPELERKIYVGHGITTSVEDKHITYALRPE----KMLV 308

Query: 299 LAPSP---ENTITGVVDVVEPLGSETILHVKVGDDLIVAS 335
               P    N   G +  +  LG  ++ +V++    +V S
Sbjct: 309 TTQQPTCEHNWSRGKIHDIAYLGGHSVFYVELPSGKVVQS 348


Lambda     K      H
   0.319    0.138    0.387 

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: 349
Number of extensions: 8
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: 369
Length of database: 380
Length adjustment: 30
Effective length of query: 339
Effective length of database: 350
Effective search space:   118650
Effective search space used:   118650
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