GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Desulfovibrio vulgaris Miyazaki F

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 8500099 DvMF_0862 ABC transporter related (RefSeq)

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Miya:8500099
          Length = 248

 Score =  190 bits (483), Expect = 3e-53
 Identities = 106/227 (46%), Positives = 146/227 (64%), Gaps = 4/227 (1%)

Query: 17  EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76
           E+ AL    L++  G+   + G SG+GKSTLLR INRLE    G I+V+G+DV + D + 
Sbjct: 21  ELTALNDVSLDVMPGEKVVICGPSGSGKSTLLRSINRLETVDKGTIIVDGQDVNSPDND- 79

Query: 77  LRRFRQRVGMIFQHFNLLSSKTVADNIAM-PLRLAGGFSRAEVDARVSELLARVGLSDHA 135
           + + RQ +GM+FQ FNL   KTV  N+ M P+RL     RAE ++R  ELL +VG+SD A
Sbjct: 80  INKIRQELGMVFQSFNLFPHKTVLQNLTMAPMRLRKT-PRAEAESRALELLKKVGISDKA 138

Query: 136 RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTI 195
             +PA LSGGQ+QRV IARALA  P I+L DE TSALDP+    VL ++  + RE  +T+
Sbjct: 139 NVFPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMVTLARE-GMTM 197

Query: 196 VLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242
           V +THEM   R V D++  MD G ++E+    D F  P+HP  ++F+
Sbjct: 198 VCVTHEMGFAREVADRIIFMDHGQVLEENAPQDFFGAPKHPRLQKFL 244


Lambda     K      H
   0.322    0.138    0.393 

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: 212
Number of extensions: 10
Number of successful extensions: 3
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: 335
Length of database: 248
Length adjustment: 26
Effective length of query: 309
Effective length of database: 222
Effective search space:    68598
Effective search space used:    68598
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: 47 (22.7 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