GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF849
          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:

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