GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Magnetospirillum magneticum AMB-1

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_000009985.1:WP_011383734.1
          Length = 452

 Score =  139 bits (350), Expect = 1e-37
 Identities = 81/197 (41%), Positives = 119/197 (60%), Gaps = 12/197 (6%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L  V  K+  G+I  ++G SGSGKSTL+R +  LI+   GEV + G          L   
Sbjct: 31  LEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGH---------LMTG 81

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162
             + +SMVFQSFAL P  TV +NV  G    GV+K +  E   + ID +GL GY++ +P 
Sbjct: 82  PAKGISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYESAYPK 141

Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQL--QRNL-AKTIVF 219
           +LSGGM+QRVG ARAL    DV+L+DE FSALD L    +++ LL+L  +R +  K I+ 
Sbjct: 142 ELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPTKGILL 201

Query: 220 ITHDLDEALRIGSEIAI 236
           ++H+++EA+ +   + +
Sbjct: 202 VSHNIEEAVSMADRVLV 218


Lambda     K      H
   0.323    0.139    0.397 

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: 292
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 275
Length of database: 452
Length adjustment: 29
Effective length of query: 246
Effective length of database: 423
Effective search space:   104058
Effective search space used:   104058
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 (21.9 bits)
S2: 49 (23.5 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