GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malE1 in Pseudomonas stutzeri RCH2

Align MalE2; aka Maltose ABC transporter, periplasmic maltose-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 GFF849 Psest_0863 Maltose-binding periplasmic proteins/domains

Query= TCDB::Q9S5Y1
         (393 letters)



>lcl|FitnessBrowser__psRCH2:GFF849 Psest_0863 Maltose-binding
           periplasmic proteins/domains
          Length = 395

 Score =  261 bits (666), Expect = 3e-74
 Identities = 148/374 (39%), Positives = 230/374 (61%), Gaps = 11/374 (2%)

Query: 18  LSQTKLTIWCS-EKQVDILQKLGEEFKAKYGIPVEVQYVDFGSIKSKFLTAAPQGQGADI 76
           + + KL +W + +K    L ++G++F A+ GIPVEV + D  S   KF  AA  G G DI
Sbjct: 27  IEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPVEVAHPD--SATDKFQQAAATGNGPDI 84

Query: 77  IVGAHDWVGELAVNGLIEPIPNFSDLKN-FYDTALKAFSYGGKLYGVPYAMEAVALIYNK 135
            + AHD +GE A +GL+ P+   +D K+   D + +A +Y  KL+G P ++E + LIYNK
Sbjct: 85  FIWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQAVTYDNKLWGYPISVETIGLIYNK 144

Query: 136 DYVDSVPKTMDELIEKAKQIDEEYGGEVRGFIYDVANFYFSAPFILGYGGYVFKETPQGL 195
             VD+ PKT D+++   +++  +     R  ++D  N YF+ P +   GGYVF+    G 
Sbjct: 145 ALVDTPPKTFDDVMALNEKLAAQ---GKRAILWDYNNTYFTWPLLSAKGGYVFEHADGGY 201

Query: 196 DVTDIGLANEGAVKGAKLIKRMIDEGVLTPGDNYGTMDSMFKEGLAAMIINGLWAIKSYK 255
           DV   G+ N GA  GA++++ +ID+GV+  G +Y   ++ F +G +AM+I+G WA  + +
Sbjct: 202 DVKSTGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEAAFNKGDSAMMISGPWAWSNIE 261

Query: 256 DAGINYGVAPIPELEPGVPAKPFVGVQGFMINAKSPNKVIAMEFLTNFIARKETMYKIYL 315
            +GI++GVAPIP ++ G P KPFVGV   ++NA SPNK +A+EFL N++ + E + K   
Sbjct: 262 KSGIDFGVAPIPAID-GEPGKPFVGVAAALLNAASPNKDLAVEFLENYLLQVEGL-KTVN 319

Query: 316 ADPRLPARKDV--LELVKDNPDVVAFTQSASMGTPMPNVPEMAPVWSAMGDALSIIINGQ 373
           AD  L A  +   +E +  NP + A  ++A MG PMPNVPEM   WS+M  AL+ I +G+
Sbjct: 320 ADVPLGAVANTAYMEELSANPHIKATFENAQMGEPMPNVPEMGAFWSSMAAALTNITSGR 379

Query: 374 ASVEDALKEAVEKI 387
             V+ AL +A ++I
Sbjct: 380 QDVDAALDDAAKRI 393


Lambda     K      H
   0.318    0.138    0.398 

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: 424
Number of extensions: 17
Number of successful extensions: 6
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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