GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Herbaspirillum seropedicae SmR1

Align 2-deoxy-D-ribonate transporter (characterized)
to candidate HSERO_RS21145 HSERO_RS21145 MFS transporter

Query= reanno::Burk376:H281DRAFT_00642
         (448 letters)



>FitnessBrowser__HerbieS:HSERO_RS21145
          Length = 437

 Score =  269 bits (688), Expect = 1e-76
 Identities = 152/408 (37%), Positives = 225/408 (55%), Gaps = 14/408 (3%)

Query: 19  RKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVP 78
           +K   R++P +   Y +++LDR NV  AKLQ++ D+G S   +G G+G+FF+GY L EVP
Sbjct: 23  KKVFWRIMPFLMLCYVIAYLDRVNVGFAKLQMSQDLGFSETVFGLGAGLFFIGYFLFEVP 82

Query: 79  SNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVT 138
           SN+  HKVG R WIARI +TWGILS A MFVQ  + FY+LR LLG+AEAG +P ++  +T
Sbjct: 83  SNILMHKVGARIWIARIMITWGILSAAFMFVQNATQFYILRFLLGLAEAGFYPGIILYLT 142

Query: 139 LWFAPHDRPVVVGWIYIAPALALMLGNPLGGALMQLDGF---GGLHGWQWMFMLEGIPSV 195
            WF  H R  V+        +A +LGNPL G +M  D F   GGL GWQWMF++E IP+V
Sbjct: 143 YWFPSHRRAKVIAVFMSGIPVAGILGNPLSGWIM--DAFHQNGGLEGWQWMFLIEAIPAV 200

Query: 196 IVGIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIG 255
           ++G+     +    + A+WL+  E+  L+  A IDG  +   S   + A +K     L+ 
Sbjct: 201 LIGVATVLYLDNDVKSAKWLNDEEKASLQ--ADIDGDAKGKESKHGFGAIVKDARVWLMC 258

Query: 256 LIYFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPRIHRRTDRD 315
           LIYF   +   GL  + P ++    V  +L +G LSA   + F   ++ +  I R  DR 
Sbjct: 259 LIYFSFVMGQYGLTLWMPTLVKATGVKGNLEIGLLSA---IPFGCAIIAMNLIGRSADRM 315

Query: 316 CVFLGILTAGLILGACAY----LAVTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGI 371
                 L    ++G   +    L   N A  IA L++ A       P +W++    L G 
Sbjct: 316 RERRWHLVIPALMGGVGFVGAALFADNTAVSIASLSLAAAGVLTCAPLFWSLPTAFLSGA 375

Query: 372 QAAAGLAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLG 419
            AA G+A +N++G + GFV PYL G  +  +  +  G  ++ +  V+G
Sbjct: 376 AAAVGIAAINSVGNLAGFVSPYLIGYLKDLTHNNATGMYMLAVMLVVG 423


Lambda     K      H
   0.329    0.142    0.436 

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: 583
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: 448
Length of database: 437
Length adjustment: 32
Effective length of query: 416
Effective length of database: 405
Effective search space:   168480
Effective search space used:   168480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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