GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malE1 in Hafnia paralvei ATCC 29927

Align MalE1; 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 WP_061059304.1 M988_RS19105 maltose/maltodextrin ABC transporter substrate-binding protein MalE

Query= TCDB::Q9X0T1
         (391 letters)



>NCBI__GCF_001655005.1:WP_061059304.1
          Length = 396

 Score =  217 bits (553), Expect = 4e-61
 Identities = 136/386 (35%), Positives = 214/386 (55%), Gaps = 12/386 (3%)

Query: 7   IALLVVSLVVLA---QPKLTIWCS-EKQVDILQKLGEEFKAKYGVEVEVQYVNFQDIKSK 62
           +A LV+S    A   + KL IW + +K  + L ++G++F+ + G++V V++ +   ++ K
Sbjct: 15  LATLVLSSSAFAKIEEGKLVIWINGDKGYNGLAEIGKKFEKETGIKVLVEHPD--KLEEK 72

Query: 63  FLTAAPEGQGADIIVGAHDWVGELAVNGLIEPI-PNFSDLKNFYETALNAFSYGGKLYGI 121
           +   A  G G DII  AHD  G  A +GL+  I P+ +     Y    +A  Y GKL   
Sbjct: 73  YPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEIHPSKAFQDKLYPFTWDAVRYNGKLIAY 132

Query: 122 PYAMEAIALIYNKDYVPEPPKTMDELIEIAKQIDEEFGGEVRGFITSAAEFYYIAPFIFG 181
           P A+EA++LIYNKD +PEPPKT +E+  + K++  +    +   + +  E Y+  P I  
Sbjct: 133 PVAVEALSLIYNKDILPEPPKTWEEIPALDKELRAKGKSAI---MWNLQEPYFTWPIIAA 189

Query: 182 YGGYVFKQTEKGLDVNDIGLANEGAIKGVKLLKRLVDEGILDPSDNYQIMDSMFREGQAA 241
            GGY FK      ++ D+G+ N G+  G++ +  LV    ++   +Y I ++ F +GQ A
Sbjct: 190 DGGYAFKYDNGTYNIKDVGVNNAGSQAGLQFIVDLVKNKHINADTDYSIAEAAFNKGQTA 249

Query: 242 MIINGPWAIKAYKDAGIDYGVAPIPDLEPGVPARPFVGVQGFMVNAKSPNKLLAIEFLTS 301
           M INGPWA      + I+YGVA +P  + G P++PFVGV    +NA SPNK LA EFL +
Sbjct: 250 MTINGPWAWSNIDKSNINYGVALLPTFK-GHPSKPFVGVLSAGINAASPNKELATEFLEN 308

Query: 302 FIAKKETMYRIYLGDP-RLPSRKDVLELVKDNPDVVGFTLSAANGIPMPNVPQMAAVWAA 360
           ++     + +I    P    + K   E ++ +P +     +A  G  MPN+PQM+A W A
Sbjct: 309 YLMTNAGLEQINKDKPLGAVALKSYQETLEKDPKIAATMQNAQKGEIMPNIPQMSAFWYA 368

Query: 361 MNDALNLVVNGKATVEEALKNAVERI 386
              A+   VNG+ +V+EAL  A +RI
Sbjct: 369 ERSAIINAVNGRQSVKEALTGAEQRI 394


Lambda     K      H
   0.319    0.139    0.404 

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: 415
Number of extensions: 30
Number of successful extensions: 5
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: 391
Length of database: 396
Length adjustment: 31
Effective length of query: 360
Effective length of database: 365
Effective search space:   131400
Effective search space used:   131400
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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