GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Ss in Pseudomonas fluorescens GW456-L13

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate PfGW456L13_5058 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5058
          Length = 326

 Score =  190 bits (482), Expect = 9e-53
 Identities = 103/259 (39%), Positives = 165/259 (63%), Gaps = 5/259 (1%)

Query: 355 VVMKILNLSKIYYIRKNLILSEP-INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAG 413
           VV+   +L++ Y + + L      + A+N VSFEL+ G   A+VG SG GKST+A+ L  
Sbjct: 3   VVLTARDLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTL 62

Query: 414 MIQQTSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHK 473
           + + +SG + + G++V+          +++VQM+FQ PY+SL+PR  V   +  PLLI+ 
Sbjct: 63  IEEPSSGSLKIAGQEVAGADKAQRKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLINT 122

Query: 474 KVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADE 533
            +S  ++   K+  ++K VGL+P  ++  +YPH  SGG+RQR+A+ARA  ++PKVLVADE
Sbjct: 123 NLSAAER-REKVQAMMKQVGLRP--EHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADE 179

Query: 534 PVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTY 592
           P S LD S++A +LNL    ++    + ++I+H++A V ++AD +MV+Y GR VE G   
Sbjct: 180 PTSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGTKE 239

Query: 593 EVISNPSHEYTKRLIEAVP 611
           ++ S P H YT+ L+ A P
Sbjct: 240 DIYSRPLHPYTQALLSATP 258



 Score =  182 bits (462), Expect = 2e-50
 Identities = 104/308 (33%), Positives = 178/308 (57%), Gaps = 9/308 (2%)

Query: 13  ELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGH 72
           E++ G F     V  +  V+FE+   +  A+ GESGCGKSTLA A+  L++ P     G 
Sbjct: 15  EVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALT-LIEEPS---SGS 70

Query: 73  VYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAA-VSHGVNVEEA 131
           + +  +++    + + ++LR K+   V Q    +L+P  K+GDQ+     ++  ++  E 
Sbjct: 71  LKIAGQEVAGADKAQRKQLR-KDVQMVFQSPYASLNPRQKVGDQLAEPLLINTNLSAAER 129

Query: 132 RKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQ 191
           R+ ++  ++ V L       YPH  SGG RQR+ +A +++L P +++ DEPT+ LDV +Q
Sbjct: 130 REKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQ 189

Query: 192 YEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPY 251
            ++L     +Q++   + V ISH+++++  ++D V +MY G  VE+G+KE+I  RP HPY
Sbjct: 190 AQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGTKEDIYSRPLHPY 249

Query: 252 TYLLISSLPSLVKRREK-LLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDI 310
           T  L+S+ P++    +K  + I G  P  L+  P+ C F+ RCP+  E+CST  PAL  +
Sbjct: 250 TQALLSATPAIHPDPDKPKIKIVGELPNPLNP-PSGCAFHKRCPYATERCSTEEPAL-RL 307

Query: 311 MDGHKARC 318
           + G +  C
Sbjct: 308 IAGRQVAC 315


Lambda     K      H
   0.319    0.138    0.391 

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: 507
Number of extensions: 20
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 326
Length adjustment: 33
Effective length of query: 584
Effective length of database: 293
Effective search space:   171112
Effective search space used:   171112
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 (21.7 bits)
S2: 51 (24.3 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