GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_2555 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 206398 DVU0966 amino acid ABC transporter, periplasmic amino acid-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>lcl|MicrobesOnline__882:206398 DVU0966 amino acid ABC transporter,
           periplasmic amino acid-binding protein
          Length = 272

 Score =  107 bits (268), Expect = 2e-28
 Identities = 78/261 (29%), Positives = 123/261 (47%), Gaps = 23/261 (8%)

Query: 8   LLASLAAAAFCTTGAQAQD---------------NVLRVGTDATFPPMEFVE-NGKRTGF 51
           LLA++  AA     A A D                 LRVG DA + P E  + NG   GF
Sbjct: 6   LLAAMMMAALLAAPAMAADIELAKKSTLNEIMARGELRVGFDAGYLPFEMTDKNGNYVGF 65

Query: 52  DIELVEAIAKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYA 111
           DI++ + +A+ MG +   V+ DF G+IP L+S +FD+ +S + +T ER   ++F D Y  
Sbjct: 66  DIDIAKEMARAMGVKFVPVNTDFDGMIPALLSDKFDIIISGMTVTQERNLKINFADPYIV 125

Query: 112 GGLVVMV--KADNKAINKLADLDGKKVSV--QVGTKSVSYLTEKFPKVQRVEVEKNQEMF 167
            G  V++  K + K +    DL+  + +V  ++GT          PK +    +K  +  
Sbjct: 126 VGQTVLLSKKLEGK-VKSWKDLNSPEYTVVSRLGTTGEEAAKRMLPKAKFKSFDKEADGA 184

Query: 168 NLVDIGRADAAVTGKP--AAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGA 225
             V  GRADA V   P    F   + +  +  LD+  T E  G  ++K  P+    +N  
Sbjct: 185 LEVVNGRADAWVYDMPFNVVFMAEQGKDKVVHLDKPFTYEPLGFGIKKGDPDFLNFLNNF 244

Query: 226 ITKLKADGTYAAIVKKWFSNS 246
           + ++K DG Y  I  KW  ++
Sbjct: 245 MRQIKNDGRYDRIYDKWMRST 265


Lambda     K      H
   0.317    0.133    0.369 

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: 164
Number of extensions: 10
Number of successful extensions: 2
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: 249
Length of database: 272
Length adjustment: 24
Effective length of query: 225
Effective length of database: 248
Effective search space:    55800
Effective search space used:    55800
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: 47 (22.7 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