GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Malonomonas rubra DSM 5091

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  311 bits (796), Expect = 2e-89
 Identities = 157/261 (60%), Positives = 201/261 (77%)

Query: 8   KIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67
           KIEVKN++KIFG + K+A+ L++Q   K+ +  +T   VGV D S  I  GEIFVIMGLS
Sbjct: 6   KIEVKNLYKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMGLS 65

Query: 68  GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127
           GSGKST+VR  NRLI+PTSG +L+DGEDI+ ++ D L + RR K+SMVFQSF L+PH +V
Sbjct: 66  GSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVFQSFALMPHMTV 125

Query: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187
           L N A+GL++ G  KQ   +RAL  +  VGL+ +    P +LSGGM+QRVGLAR LA D 
Sbjct: 126 LQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQRVGLARGLAVDP 185

Query: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247
           DI+LMDEAFSALDPLIR EMQD+LL+LQ    +TIVFI+HDLDEA+RIG+RIAI++ G++
Sbjct: 186 DILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGGRV 245

Query: 248 IQVGTPREILHSPADEYVDRF 268
           +QVGTP EIL +PAD+YV  F
Sbjct: 246 VQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.321    0.138    0.387 

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: 345
Number of extensions: 19
Number of successful extensions: 1
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: 276
Length of database: 415
Length adjustment: 28
Effective length of query: 248
Effective length of database: 387
Effective search space:    95976
Effective search space used:    95976
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 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