GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Sinorhizobium fredii NGR234

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>NCBI__GCF_000018545.1:WP_015887278.1
          Length = 360

 Score =  228 bits (582), Expect = 1e-64
 Identities = 124/322 (38%), Positives = 191/322 (59%), Gaps = 6/322 (1%)

Query: 24  LLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIA 83
           L  + +  E G    LLG SGCGK+T+LNI++GL  PS G +L   R +  A P++R+IA
Sbjct: 19  LKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSILGAHPKDRDIA 78

Query: 84  QVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADA 143
            VFQ   +Y  M+VA N+ F L  RKVP  + ++ V   A +L++   L+++ + L+   
Sbjct: 79  MVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTARLLQIENLLDRKPSQLSGGQ 138

Query: 144 KQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEA 203
           +Q++++GR LVR +    LFDEPL+ +D  L+ ++R +LK++H  LK T++YVTHDQ+EA
Sbjct: 139 RQRVAIGRALVR-EPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLKTTVVYVTHDQIEA 197

Query: 204 LTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGHR 263
           +T A ++ VM  G+  Q+G+   +++RPA  +V  F+GSP MN L A   G  L + G  
Sbjct: 198 MTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPPMNILDAEGTGSGLRILGSE 257

Query: 264 LASPVGRALPAGA----LQVGIRPEYLALAQPQQAGALPGTVVQVQDI-GTYQMLTAKVG 318
              P+G A P G     ++VGIRPE L LA     G     +V+V ++ G   ++TA++G
Sbjct: 258 NTLPLGGAFPNGTTGRRVKVGIRPEALRLAGDDATGGRLTAIVEVMELTGPELVITARIG 317

Query: 319 EHTVKARFTPETRLPSSGDTAW 340
           E  + A   P T L      A+
Sbjct: 318 EQRITACLPPRTSLEPGSTQAF 339


Lambda     K      H
   0.320    0.136    0.395 

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: 315
Number of extensions: 15
Number of successful extensions: 4
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: 358
Length of database: 360
Length adjustment: 29
Effective length of query: 329
Effective length of database: 331
Effective search space:   108899
Effective search space used:   108899
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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